[English] 日本語
Yorodumi
- PDB-6fqj: GluA2(flop) G724C ligand binding core dimer bound to ZK200775 at ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fqj
TitleGluA2(flop) G724C ligand binding core dimer bound to ZK200775 at 2.50 Angstrom resolution
ComponentsGlutamate receptor 2,Glutamate receptor 2
KeywordsMEMBRANE PROTEIN / AMPAR receptor / Ligand binding domain / Competitive antagonist / Cross-linked dimer
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / immunoglobulin binding / Trafficking of GluR2-containing AMPA receptors / response to lithium ion ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / immunoglobulin binding / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / kainate selective glutamate receptor activity / AMPA glutamate receptor complex / cellular response to glycine / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor complex / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / response to fungicide / regulation of synaptic transmission, glutamatergic / glutamate-gated receptor activity / cytoskeletal protein binding / ionotropic glutamate receptor binding / extracellular ligand-gated monoatomic ion channel activity / presynaptic active zone membrane / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / glutamate-gated calcium ion channel activity / dendrite cytoplasm / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor signaling pathway / SNARE binding / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / protein tetramerization / establishment of protein localization / synaptic membrane / modulation of chemical synaptic transmission / postsynaptic density membrane / terminal bouton / cerebral cortex development / Schaffer collateral - CA1 synapse / receptor internalization / synaptic vesicle membrane / synaptic vesicle / presynapse / signaling receptor activity / amyloid-beta binding / presynaptic membrane / growth cone / scaffold protein binding / chemical synaptic transmission / perikaryon / dendritic spine / postsynaptic membrane / neuron projection / postsynaptic density / axon / neuronal cell body / synapse / dendrite / protein-containing complex binding / protein kinase binding / glutamatergic synapse / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region ...Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-ZK1 / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.50001683981 Å
AuthorsCoombs, I.D. / Soto, D. / Gold, M.G. / Farrant, M.F. / Cull-Candy, S.G.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/J002976/1 United Kingdom
Medical Research Council (United Kingdom)MR/J012998/1 United Kingdom
Wellcome Trust086185/Z/08/Z United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: Homomeric GluA2(R) AMPA receptors can conduct when desensitized.
Authors: Coombs, I.D. / Soto, D. / McGee, T.P. / Gold, M.G. / Farrant, M. / Cull-Candy, S.G.
History
DepositionFeb 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamate receptor 2,Glutamate receptor 2
B: Glutamate receptor 2,Glutamate receptor 2
C: Glutamate receptor 2,Glutamate receptor 2
D: Glutamate receptor 2,Glutamate receptor 2
E: Glutamate receptor 2,Glutamate receptor 2
F: Glutamate receptor 2,Glutamate receptor 2
G: Glutamate receptor 2,Glutamate receptor 2
H: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,87316
Polymers234,5998
Non-polymers3,2748
Water14,862825
1
A: Glutamate receptor 2,Glutamate receptor 2
H: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4684
Polymers58,6502
Non-polymers8192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-14 kcal/mol
Surface area24230 Å2
MethodPISA
2
B: Glutamate receptor 2,Glutamate receptor 2
G: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4684
Polymers58,6502
Non-polymers8192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-15 kcal/mol
Surface area23860 Å2
MethodPISA
3
C: Glutamate receptor 2,Glutamate receptor 2
E: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4684
Polymers58,6502
Non-polymers8192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-15 kcal/mol
Surface area23860 Å2
MethodPISA
4
D: Glutamate receptor 2,Glutamate receptor 2
F: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4684
Polymers58,6502
Non-polymers8192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-15 kcal/mol
Surface area23610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.010, 144.290, 199.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRHISHIS(chain 'A' and (resid 5 through 23 or resid 26...AA5 - 235 - 23
12LEULEUALAALA(chain 'A' and (resid 5 through 23 or resid 26...AA26 - 4426 - 44
13HISHISALAALA(chain 'A' and (resid 5 through 23 or resid 26...AA46 - 6346 - 63
14ASPASPALAALA(chain 'A' and (resid 5 through 23 or resid 26...AA65 - 6665 - 66
15THRTHRTHRTHR(chain 'A' and (resid 5 through 23 or resid 26...AA6868
16ILEILEILEILE(chain 'A' and (resid 5 through 23 or resid 26...AA70 - 12170 - 121
17SERSERSERSER(chain 'A' and (resid 5 through 23 or resid 26...AA123 - 128123 - 128
18GLNGLNTHRTHR(chain 'A' and (resid 5 through 23 or resid 26...AA130 - 131130 - 131
19ILEILEPHEPHE(chain 'A' and (resid 5 through 23 or resid 26...AA133 - 147133 - 147
110SERSERSERSER(chain 'A' and (resid 5 through 23 or resid 26...AA150150
111ILEILEMETMET(chain 'A' and (resid 5 through 23 or resid 26...AA152 - 162152 - 162
112SERSERVALVAL(chain 'A' and (resid 5 through 23 or resid 26...AA164 - 171164 - 171
113THRTHRARGARG(chain 'A' and (resid 5 through 23 or resid 26...AA173 - 182173 - 182
114SERSERLYSLYS(chain 'A' and (resid 5 through 23 or resid 26...AA184 - 185184 - 185
115TYRTYRLEULEU(chain 'A' and (resid 5 through 23 or resid 26...AA188 - 192188 - 192
116SERSERARGARG(chain 'A' and (resid 5 through 23 or resid 26...AA194 - 203194 - 203
117PROPROTHRTHR(chain 'A' and (resid 5 through 23 or resid 26...AA205 - 208205 - 208
118LYSLYSSERSER(chain 'A' and (resid 5 through 23 or resid 26...AA210 - 217210 - 217
119GLYGLYGLUGLU(chain 'A' and (resid 5 through 23 or resid 26...AA219 - 243219 - 243
120GLYGLYTYRTYR(chain 'A' and (resid 5 through 23 or resid 26...AA245 - 256245 - 256
121GLYGLYCYSCYS(chain 'A' and (resid 5 through 23 or resid 26...AA259 - 261259 - 261
222THRTHRHISHIS(chain 'B' and (resid 5 through 23 or resid 26...BB5 - 235 - 23
223LEULEUALAALA(chain 'B' and (resid 5 through 23 or resid 26...BB26 - 4426 - 44
224HISHISALAALA(chain 'B' and (resid 5 through 23 or resid 26...BB46 - 6346 - 63
225ASPASPALAALA(chain 'B' and (resid 5 through 23 or resid 26...BB65 - 6665 - 66
226THRTHRTHRTHR(chain 'B' and (resid 5 through 23 or resid 26...BB6868
227ILEILEILEILE(chain 'B' and (resid 5 through 23 or resid 26...BB70 - 12170 - 121
228SERSERSERSER(chain 'B' and (resid 5 through 23 or resid 26...BB123 - 128123 - 128
229GLNGLNTHRTHR(chain 'B' and (resid 5 through 23 or resid 26...BB130 - 131130 - 131
230ILEILEPHEPHE(chain 'B' and (resid 5 through 23 or resid 26...BB133 - 147133 - 147
231SERSERSERSER(chain 'B' and (resid 5 through 23 or resid 26...BB150150
232ILEILEMETMET(chain 'B' and (resid 5 through 23 or resid 26...BB152 - 162152 - 162
233SERSERVALVAL(chain 'B' and (resid 5 through 23 or resid 26...BB164 - 171164 - 171
234THRTHRARGARG(chain 'B' and (resid 5 through 23 or resid 26...BB173 - 182173 - 182
235SERSERLYSLYS(chain 'B' and (resid 5 through 23 or resid 26...BB184 - 185184 - 185
236TYRTYRLEULEU(chain 'B' and (resid 5 through 23 or resid 26...BB188 - 192188 - 192
237SERSERARGARG(chain 'B' and (resid 5 through 23 or resid 26...BB194 - 203194 - 203
238PROPROTHRTHR(chain 'B' and (resid 5 through 23 or resid 26...BB205 - 208205 - 208
239LYSLYSSERSER(chain 'B' and (resid 5 through 23 or resid 26...BB210 - 217210 - 217
240GLYGLYGLUGLU(chain 'B' and (resid 5 through 23 or resid 26...BB219 - 243219 - 243
241GLYGLYTYRTYR(chain 'B' and (resid 5 through 23 or resid 26...BB245 - 256245 - 256
242GLYGLYCYSCYS(chain 'B' and (resid 5 through 23 or resid 26...BB259 - 261259 - 261
343THRTHRHISHIS(chain 'C' and (resid 5 through 23 or resid 26...CC5 - 235 - 23
344LEULEUALAALA(chain 'C' and (resid 5 through 23 or resid 26...CC26 - 4426 - 44
345HISHISALAALA(chain 'C' and (resid 5 through 23 or resid 26...CC46 - 6346 - 63
346ASPASPALAALA(chain 'C' and (resid 5 through 23 or resid 26...CC65 - 6665 - 66
347THRTHRTHRTHR(chain 'C' and (resid 5 through 23 or resid 26...CC6868
348ILEILEILEILE(chain 'C' and (resid 5 through 23 or resid 26...CC70 - 12170 - 121
349SERSERSERSER(chain 'C' and (resid 5 through 23 or resid 26...CC123 - 128123 - 128
350GLNGLNTHRTHR(chain 'C' and (resid 5 through 23 or resid 26...CC130 - 131130 - 131
351ILEILEPHEPHE(chain 'C' and (resid 5 through 23 or resid 26...CC133 - 147133 - 147
352SERSERSERSER(chain 'C' and (resid 5 through 23 or resid 26...CC150150
353ILEILEMETMET(chain 'C' and (resid 5 through 23 or resid 26...CC152 - 162152 - 162
354SERSERVALVAL(chain 'C' and (resid 5 through 23 or resid 26...CC164 - 171164 - 171
355THRTHRARGARG(chain 'C' and (resid 5 through 23 or resid 26...CC173 - 182173 - 182
356SERSERLYSLYS(chain 'C' and (resid 5 through 23 or resid 26...CC184 - 185184 - 185
357TYRTYRLEULEU(chain 'C' and (resid 5 through 23 or resid 26...CC188 - 192188 - 192
358SERSERARGARG(chain 'C' and (resid 5 through 23 or resid 26...CC194 - 203194 - 203
359PROPROTHRTHR(chain 'C' and (resid 5 through 23 or resid 26...CC205 - 208205 - 208
360LYSLYSSERSER(chain 'C' and (resid 5 through 23 or resid 26...CC210 - 217210 - 217
361GLYGLYGLUGLU(chain 'C' and (resid 5 through 23 or resid 26...CC219 - 243219 - 243
362GLYGLYTYRTYR(chain 'C' and (resid 5 through 23 or resid 26...CC245 - 256245 - 256
363GLYGLYCYSCYS(chain 'C' and (resid 5 through 23 or resid 26...CC259 - 261259 - 261
464THRTHRHISHIS(chain 'D' and (resid 5 through 20 or (resid 21...DD5 - 235 - 23
465LEULEUALAALA(chain 'D' and (resid 5 through 20 or (resid 21...DD26 - 4426 - 44
466HISHISALAALA(chain 'D' and (resid 5 through 20 or (resid 21...DD46 - 6346 - 63
467ASPASPALAALA(chain 'D' and (resid 5 through 20 or (resid 21...DD65 - 6665 - 66
468THRTHRTHRTHR(chain 'D' and (resid 5 through 20 or (resid 21...DD6868
469ILEILEILEILE(chain 'D' and (resid 5 through 20 or (resid 21...DD70 - 12170 - 121
470SERSERSERSER(chain 'D' and (resid 5 through 20 or (resid 21...DD123 - 128123 - 128
471GLNGLNTHRTHR(chain 'D' and (resid 5 through 20 or (resid 21...DD130 - 131130 - 131
472ILEILEPHEPHE(chain 'D' and (resid 5 through 20 or (resid 21...DD133 - 147133 - 147
473SERSERSERSER(chain 'D' and (resid 5 through 20 or (resid 21...DD150150
474ILEILEMETMET(chain 'D' and (resid 5 through 20 or (resid 21...DD152 - 162152 - 162
475SERSERVALVAL(chain 'D' and (resid 5 through 20 or (resid 21...DD164 - 171164 - 171
476THRTHRARGARG(chain 'D' and (resid 5 through 20 or (resid 21...DD173 - 182173 - 182
477SERSERLYSLYS(chain 'D' and (resid 5 through 20 or (resid 21...DD184 - 185184 - 185
478TYRTYRLEULEU(chain 'D' and (resid 5 through 20 or (resid 21...DD188 - 192188 - 192
479SERSERARGARG(chain 'D' and (resid 5 through 20 or (resid 21...DD194 - 203194 - 203
480PROPROTHRTHR(chain 'D' and (resid 5 through 20 or (resid 21...DD205 - 208205 - 208
481LYSLYSSERSER(chain 'D' and (resid 5 through 20 or (resid 21...DD210 - 217210 - 217
482GLYGLYGLUGLU(chain 'D' and (resid 5 through 20 or (resid 21...DD219 - 243219 - 243
483GLYGLYTYRTYR(chain 'D' and (resid 5 through 20 or (resid 21...DD245 - 256245 - 256
484GLYGLYCYSCYS(chain 'D' and (resid 5 through 20 or (resid 21...DD259 - 261259 - 261
585THRTHRHISHIS(chain 'E' and (resid 5 through 20 or (resid 21...EE5 - 235 - 23
586LEULEUALAALA(chain 'E' and (resid 5 through 20 or (resid 21...EE26 - 4426 - 44
587HISHISALAALA(chain 'E' and (resid 5 through 20 or (resid 21...EE46 - 6346 - 63
588ASPASPALAALA(chain 'E' and (resid 5 through 20 or (resid 21...EE65 - 6665 - 66
589THRTHRTHRTHR(chain 'E' and (resid 5 through 20 or (resid 21...EE6868
590ILEILEILEILE(chain 'E' and (resid 5 through 20 or (resid 21...EE70 - 12170 - 121
591SERSERSERSER(chain 'E' and (resid 5 through 20 or (resid 21...EE123 - 128123 - 128
592GLNGLNTHRTHR(chain 'E' and (resid 5 through 20 or (resid 21...EE130 - 131130 - 131
593ILEILEPHEPHE(chain 'E' and (resid 5 through 20 or (resid 21...EE133 - 147133 - 147
594SERSERSERSER(chain 'E' and (resid 5 through 20 or (resid 21...EE150150
595ILEILEMETMET(chain 'E' and (resid 5 through 20 or (resid 21...EE152 - 162152 - 162
596SERSERVALVAL(chain 'E' and (resid 5 through 20 or (resid 21...EE164 - 171164 - 171
597THRTHRARGARG(chain 'E' and (resid 5 through 20 or (resid 21...EE173 - 182173 - 182
598SERSERLYSLYS(chain 'E' and (resid 5 through 20 or (resid 21...EE184 - 185184 - 185
599TYRTYRLEULEU(chain 'E' and (resid 5 through 20 or (resid 21...EE188 - 192188 - 192
5100SERSERARGARG(chain 'E' and (resid 5 through 20 or (resid 21...EE194 - 203194 - 203
5101PROPROTHRTHR(chain 'E' and (resid 5 through 20 or (resid 21...EE205 - 208205 - 208
5102LYSLYSSERSER(chain 'E' and (resid 5 through 20 or (resid 21...EE210 - 217210 - 217
5103GLYGLYGLUGLU(chain 'E' and (resid 5 through 20 or (resid 21...EE219 - 243219 - 243
5104GLYGLYTYRTYR(chain 'E' and (resid 5 through 20 or (resid 21...EE245 - 256245 - 256
5105GLYGLYCYSCYS(chain 'E' and (resid 5 through 20 or (resid 21...EE259 - 261259 - 261
6106THRTHRHISHIS(chain 'F' and (resid 5 through 23 or resid 26...FF5 - 235 - 23
6107LEULEUALAALA(chain 'F' and (resid 5 through 23 or resid 26...FF26 - 4426 - 44
6108HISHISALAALA(chain 'F' and (resid 5 through 23 or resid 26...FF46 - 6346 - 63
6109ASPASPALAALA(chain 'F' and (resid 5 through 23 or resid 26...FF65 - 6665 - 66
6110THRTHRTHRTHR(chain 'F' and (resid 5 through 23 or resid 26...FF6868
6111ILEILEILEILE(chain 'F' and (resid 5 through 23 or resid 26...FF70 - 12170 - 121
6112SERSERSERSER(chain 'F' and (resid 5 through 23 or resid 26...FF123 - 128123 - 128
6113GLNGLNTHRTHR(chain 'F' and (resid 5 through 23 or resid 26...FF130 - 131130 - 131
6114ILEILEPHEPHE(chain 'F' and (resid 5 through 23 or resid 26...FF133 - 147133 - 147
6115SERSERSERSER(chain 'F' and (resid 5 through 23 or resid 26...FF150150
6116ILEILEMETMET(chain 'F' and (resid 5 through 23 or resid 26...FF152 - 162152 - 162
6117SERSERVALVAL(chain 'F' and (resid 5 through 23 or resid 26...FF164 - 171164 - 171
6118THRTHRARGARG(chain 'F' and (resid 5 through 23 or resid 26...FF173 - 182173 - 182
6119SERSERLYSLYS(chain 'F' and (resid 5 through 23 or resid 26...FF184 - 185184 - 185
6120TYRTYRLEULEU(chain 'F' and (resid 5 through 23 or resid 26...FF188 - 192188 - 192
6121SERSERARGARG(chain 'F' and (resid 5 through 23 or resid 26...FF194 - 203194 - 203
6122PROPROTHRTHR(chain 'F' and (resid 5 through 23 or resid 26...FF205 - 208205 - 208
6123LYSLYSSERSER(chain 'F' and (resid 5 through 23 or resid 26...FF210 - 217210 - 217
6124GLYGLYGLUGLU(chain 'F' and (resid 5 through 23 or resid 26...FF219 - 243219 - 243
6125GLYGLYTYRTYR(chain 'F' and (resid 5 through 23 or resid 26...FF245 - 256245 - 256
6126GLYGLYCYSCYS(chain 'F' and (resid 5 through 23 or resid 26...FF259 - 261259 - 261
7127THRTHRHISHIS(chain 'G' and (resid 5 through 20 or (resid 21...GG5 - 235 - 23
7128LEULEUALAALA(chain 'G' and (resid 5 through 20 or (resid 21...GG26 - 4426 - 44
7129HISHISALAALA(chain 'G' and (resid 5 through 20 or (resid 21...GG46 - 6346 - 63
7130ASPASPALAALA(chain 'G' and (resid 5 through 20 or (resid 21...GG65 - 6665 - 66
7131THRTHRTHRTHR(chain 'G' and (resid 5 through 20 or (resid 21...GG6868
7132ILEILEILEILE(chain 'G' and (resid 5 through 20 or (resid 21...GG70 - 12170 - 121
7133SERSERSERSER(chain 'G' and (resid 5 through 20 or (resid 21...GG123 - 128123 - 128
7134GLNGLNTHRTHR(chain 'G' and (resid 5 through 20 or (resid 21...GG130 - 131130 - 131
7135ILEILEPHEPHE(chain 'G' and (resid 5 through 20 or (resid 21...GG133 - 147133 - 147
7136SERSERSERSER(chain 'G' and (resid 5 through 20 or (resid 21...GG150150
7137ILEILEMETMET(chain 'G' and (resid 5 through 20 or (resid 21...GG152 - 162152 - 162
7138SERSERVALVAL(chain 'G' and (resid 5 through 20 or (resid 21...GG164 - 171164 - 171
7139THRTHRARGARG(chain 'G' and (resid 5 through 20 or (resid 21...GG173 - 182173 - 182
7140SERSERLYSLYS(chain 'G' and (resid 5 through 20 or (resid 21...GG184 - 185184 - 185
7141TYRTYRLEULEU(chain 'G' and (resid 5 through 20 or (resid 21...GG188 - 192188 - 192
7142SERSERARGARG(chain 'G' and (resid 5 through 20 or (resid 21...GG194 - 203194 - 203
7143PROPROTHRTHR(chain 'G' and (resid 5 through 20 or (resid 21...GG205 - 208205 - 208
7144LYSLYSSERSER(chain 'G' and (resid 5 through 20 or (resid 21...GG210 - 217210 - 217
7145GLYGLYGLUGLU(chain 'G' and (resid 5 through 20 or (resid 21...GG219 - 243219 - 243
7146GLYGLYTYRTYR(chain 'G' and (resid 5 through 20 or (resid 21...GG245 - 256245 - 256
7147GLYGLYCYSCYS(chain 'G' and (resid 5 through 20 or (resid 21...GG259 - 261259 - 261
8148THRTHRHISHIS(chain 'H' and (resid 5 through 20 or (resid 21...HH5 - 235 - 23
8149LEULEUALAALA(chain 'H' and (resid 5 through 20 or (resid 21...HH26 - 4426 - 44
8150HISHISALAALA(chain 'H' and (resid 5 through 20 or (resid 21...HH46 - 6346 - 63
8151ASPASPALAALA(chain 'H' and (resid 5 through 20 or (resid 21...HH65 - 6665 - 66
8152THRTHRTHRTHR(chain 'H' and (resid 5 through 20 or (resid 21...HH6868
8153ILEILEILEILE(chain 'H' and (resid 5 through 20 or (resid 21...HH70 - 12170 - 121
8154SERSERSERSER(chain 'H' and (resid 5 through 20 or (resid 21...HH123 - 128123 - 128
8155GLNGLNTHRTHR(chain 'H' and (resid 5 through 20 or (resid 21...HH130 - 131130 - 131
8156ILEILEPHEPHE(chain 'H' and (resid 5 through 20 or (resid 21...HH133 - 147133 - 147
8157SERSERSERSER(chain 'H' and (resid 5 through 20 or (resid 21...HH150150
8158ILEILEMETMET(chain 'H' and (resid 5 through 20 or (resid 21...HH152 - 162152 - 162
8159SERSERVALVAL(chain 'H' and (resid 5 through 20 or (resid 21...HH164 - 171164 - 171
8160THRTHRARGARG(chain 'H' and (resid 5 through 20 or (resid 21...HH173 - 182173 - 182
8161SERSERLYSLYS(chain 'H' and (resid 5 through 20 or (resid 21...HH184 - 185184 - 185
8162TYRTYRLEULEU(chain 'H' and (resid 5 through 20 or (resid 21...HH188 - 192188 - 192
8163SERSERARGARG(chain 'H' and (resid 5 through 20 or (resid 21...HH194 - 203194 - 203
8164PROPROTHRTHR(chain 'H' and (resid 5 through 20 or (resid 21...HH205 - 208205 - 208
8165LYSLYSSERSER(chain 'H' and (resid 5 through 20 or (resid 21...HH210 - 217210 - 217
8166GLYGLYGLUGLU(chain 'H' and (resid 5 through 20 or (resid 21...HH219 - 243219 - 243
8167GLYGLYTYRTYR(chain 'H' and (resid 5 through 20 or (resid 21...HH245 - 256245 - 256
8168GLYGLYCYSCYS(chain 'H' and (resid 5 through 20 or (resid 21...HH259 - 261259 - 261

-
Components

#1: Protein
Glutamate receptor 2,Glutamate receptor 2 / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / ...GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2


Mass: 29324.826 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET22b / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): Origami B / References: UniProt: P19491
#2: Chemical
ChemComp-ZK1 / {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid / [[3,4-Dihydro-7-(4-morpholinyl)-2,3-dioxo-6-(trifluorom ethyl)-1(2H)-quinoxalinyl]methyl]phosphonic acid


Mass: 409.254 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H15F3N3O6P / Comment: antagonist, medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 825 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium Chloride, 20% PEG 3350, 10microM ZK200775.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.258769→81.83 Å / Num. obs: 114724 / % possible obs: 99.9 % / Redundancy: 1.9 % / CC1/2: 0.985 / Rpim(I) all: 0.086 / Rrim(I) all: 0.121 / Net I/σ(I): 6.8
Reflection shellResolution: 2.26→2.34 Å

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimlessdata scaling
PHASERphasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KGC

3kgc


Resolution: 2.50001683981→81.83 Å / SU ML: 0.351067286516 / Cross valid method: FREE R-VALUE / σ(F): 1.33646103558 / Phase error: 27.6175650896
RfactorNum. reflection% reflection
Rfree0.264914925023 8191 4.98505882138 %
Rwork0.197587956151 --
obs0.2009259541 86340 99.1665258431 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 55.2256097443 Å2
Refinement stepCycle: LAST / Resolution: 2.50001683981→81.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16159 0 216 825 17200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01259804673616691
X-RAY DIFFRACTIONf_angle_d1.2736999694922514
X-RAY DIFFRACTIONf_chiral_restr0.06239347720732457
X-RAY DIFFRACTIONf_plane_restr0.007886230020142778
X-RAY DIFFRACTIONf_dihedral_angle_d15.717416709410064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.52840.3128904394822920.2761443724725282X-RAY DIFFRACTION99.4824201321
2.5284-2.55820.3228318062452800.2568489536545152X-RAY DIFFRACTION99.7246190564
2.5582-2.58940.335070223612440.2621736895625293X-RAY DIFFRACTION99.7298270893
2.5894-2.62220.3420906945012770.2748481006285211X-RAY DIFFRACTION99.4383040406
2.6222-2.65670.3366498010092950.2803362857415210X-RAY DIFFRACTION99.3323709852
2.6567-2.69310.349143323532810.2791861617635026X-RAY DIFFRACTION96.6490621016
2.6931-2.73150.317400195242700.2459455879715206X-RAY DIFFRACTION99.5455371751
2.7315-2.77230.2946438864082460.2442478326845333X-RAY DIFFRACTION99.6072129977
2.7723-2.81560.3294366865182450.2550368367135144X-RAY DIFFRACTION99.5198522622
2.8156-2.86180.3717882878332760.2506886143725267X-RAY DIFFRACTION99.1947029349
2.8618-2.91110.3107834314092820.2473247553835152X-RAY DIFFRACTION99.4145627516
2.9111-2.96410.3003993957813050.2436880169315231X-RAY DIFFRACTION99.2292525542
2.9641-3.02110.3131163613992580.241470608845209X-RAY DIFFRACTION99.3819305581
3.0211-3.08280.3362492070682640.2386353544135228X-RAY DIFFRACTION99.2948833846
3.0828-3.14980.2946913387662740.2229237027545187X-RAY DIFFRACTION99.4717668488
3.1498-3.22310.3169016286512890.2160730536765223X-RAY DIFFRACTION99.0654205607
3.2231-3.30370.27615565693250.2070141477295193X-RAY DIFFRACTION99.4234234234
3.3037-3.3930.3077049260032600.2033733278055197X-RAY DIFFRACTION99.4895168642
3.393-3.49280.2769294979822550.2054651999215124X-RAY DIFFRACTION97.2694394213
3.4928-3.60560.2377411602252820.1891146446835209X-RAY DIFFRACTION99.5467730239
3.6056-3.73440.2740340709863210.1878520109795100X-RAY DIFFRACTION98.0289330922
3.7344-3.8840.2671213417022770.1856422547795190X-RAY DIFFRACTION99.273651716
3.884-4.06070.216050193772390.1656170477435139X-RAY DIFFRACTION97.4981870921
4.0607-4.27480.2324107155112230.1435626771575289X-RAY DIFFRACTION99.5844625113
4.2748-4.54260.1702332518722180.1300726070445297X-RAY DIFFRACTION99.2978033849
4.5426-4.89330.1960712398152920.1375402498155125X-RAY DIFFRACTION99.4127362819
4.8933-5.38570.2143234947172880.1537829140055265X-RAY DIFFRACTION99.5518106848
5.3857-6.16480.2617843607252560.1962597691615236X-RAY DIFFRACTION99.8001090314
6.1648-7.7660.2382252024942690.1689616991135239X-RAY DIFFRACTION99.6923076923
7.766-82.00670.1832130559473080.1680018670275163X-RAY DIFFRACTION99.1841914431
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.67890191098-0.6455034607810.3965018951030.659199437124-0.1747363061030.6620134583960.03302236399440.03420531878070.1676751406120.0341441365049-0.0591518658916-0.00702850791983-0.0507862573689-0.1242465234710.08066492942460.303989684737-0.01743916267210.03437663253920.287707284572-0.05064060526930.2598067667714.2308009147224.901720973320.4962830987
20.822745659357-0.626024042307-0.4772225476183.739676978630.6668062678782.483626103280.0153732770424-0.032659138956-0.1356500624770.190898480875-0.19021302061-0.07565955000320.2478135310140.009865269622840.1386547960230.322511568876-0.02597567873670.001487447778250.2824939290740.02640084121010.23998146448519.390770433313.850706164335.5340113928
31.219651435430.4821008619160.2456690136212.310663171910.7475073404634.251198006760.01048500867090.06057200233220.0521289877416-0.190637201438-0.104138365831-0.294613679559-0.0976502055606-0.1346112281990.06631572876080.1963145239980.01942092502840.02309236548270.3070151065220.03727510843720.3224503679212.966287845131.51657457917.6561288071
42.177899280090.963084027969-0.3312678263283.044854029480.7360515827640.7587104038660.05851915781390.271253478737-0.304162966072-0.211936010063-0.006028669273230.103797214670.00767472604969-0.0743474005526-0.00751009468860.2535276119890.00591567769669-0.02610511447880.226796035717-0.03094212829970.26726725775-0.277548697526-33.007937872127.8666288395
52.081782756340.0482209024348-0.7987074377641.07269908338-0.7535481810890.9754798082620.123090926315-0.01743338829880.00736732562825-0.09819171384480.1749181940320.1153597130190.2085808497080.123555070947-0.1143586046550.2978078663750.00506331930314-0.09066957682680.200774896974-0.03772617500130.3022881060413.7004813022-25.619528275928.415522757
61.726549196950.183574698351-1.172472978733.07258578346-0.2961756402083.466234476760.1749522834340.2343504045020.164426302148-0.138645267328-0.08762962185760.135085789138-0.194359339399-0.00410497813081-0.008493188131630.2810246886380.09202929112020.0198941584640.3415732238280.03725373062590.20786586056920.3979798023-20.834394740412.0877422527
71.66747184736-0.283979872581-0.9249649488852.576779245330.8057950992123.923606655080.07177699777970.00410800540196-0.223735840720.156361630875-0.132276566793-0.122599790530.2211810306090.238305336783-0.04008215885110.2046590955920.0162223701878-0.02928249516960.184347367809-0.001775948685940.28566434889312.3722561041-37.838468376830.6476351932
81.33619534874-0.457644026337-0.204412518490.742787368742-0.4769792908720.444944223510.0734566737016-0.2440297937070.4719824010050.01460047098710.027532326954-0.145556232445-0.1870803382490.0711457180356-0.005892545392080.303787929678-0.02224727023360.03375970550640.294696951455-0.07973118538980.4649340944691.92420231372-1.2522901966151.1599908243
91.29732108135-0.04377069016210.6296578533172.047618029940.1712044522651.278252589850.1393726697460.2583662716150.368891718595-0.5063993149470.277503800455-0.368312851742-0.302757261122-0.158925138781-0.05482159566470.47475604140.03074543235180.1993492423160.245751508780.08077136732320.501155869113-13.285149838410.84049528937.3035571178
100.0496992665512-0.19530733567-0.08112050514373.75056249718-0.01313393413280.978336911914-0.0310059341683-0.3665797175840.2568720637210.1320431027510.2338458949460.00731143030731-0.01250752572310.129959308294-0.05668296498430.249091455314-0.002589892750180.053941057470.317762842332-0.1055945217570.364518858857-6.42225597479-3.0436803031558.382020038
111.586845489160.163455230934-1.079658830640.9540044584021.022925779752.106189794070.0578956349971-0.07127046149390.0728631066442-0.0991438879495-0.02242554798370.007520911380370.06707321765150.0203690080349-0.04044425158720.2082802974230.0171271135661-0.007387267868250.227841632651-0.01236864236170.301077227815-26.44454412317.30650672594.59125223709
122.872306527710.271987868069-0.2416327937052.00901143129-0.1731610180512.02287487781-0.0482774490520.1039131187230.0707758483675-0.502374257606-0.1564457302320.0613801873503-0.1935844692960.0443885260811-0.04089100033290.3054347771550.027579988771-0.00697531028990.236440756417-0.004776310634590.226822496829-19.734986903518.0603247728-9.43333560445
133.535378379170.963228507751-0.1742105988291.195178876640.06188398221730.01789746903530.04421749984980.0160894727294-0.1272696242330.0412943738202-0.05982797972090.05874415082570.0556779375542-0.0272419541725-0.02866198060830.348209776801-0.03566509161550.00906435015220.260395379898-0.003059625237510.205150130356-22.2790082549-0.499622704587-5.55444021392
141.33178008897-0.1005622704-1.080278934020.2387055948540.4454019931171.42474489909-0.01781615705110.26876978332-0.345630998753-0.0564060162722-0.1028547829730.1078940515590.0791652409814-0.2785414791510.1619394015280.246260781749-0.00958620708278-0.01203015305860.285948685564-0.04170965909330.222962826636-31.7567983613-7.15321521289-11.7975219484
152.095332199911.01670037750.1364039832681.68128154869-0.9861998678541.416157774280.154728118283-0.09923220008870.1582694694760.198097577628-0.03529214118-0.147703161823-0.0237301747457-0.0279864932397-0.06581270496490.1938997794370.02811257650940.08777747404530.230274685195-0.05477572968240.215027064231-18.83113485936.691501023776.36929959923
161.96590718626-0.101931817391.131644050950.8816254960720.8168785362731.495128871370.1306790569340.0670001386112-0.2717334965820.0901913237395-0.04024330482770.02955127578430.0885896980824-0.2015857436690.003429513145530.224345938636-0.01554326937130.01558048574060.206429959149-0.009499938009570.261642661939-27.0949748101-24.398973118543.8587681903
171.8557855205-0.226507815978-0.4057907206673.26345274461-0.5672334746042.738272973880.0292559331397-0.2499380268270.03772627463220.2222271149630.003014891558550.1537845334680.371786881647-0.266053550960.103394665650.238908623034-0.03832839092540.04132186155430.2875949505160.02370192442820.221434525337-19.847709989-25.841391240557.4927573845
183.80529679461-1.93443255845-0.09673410615062.765736212730.1652261977770.752333705252-0.00731948671555-0.04709825769480.4200829172650.3213772684060.01084506040690.001619298767510.0203616176979-0.0706983860680.0367784583820.270737647034-0.009721670793330.05297954732360.252919718894-0.02901452409350.251552121763-22.5056502865-7.2061537911454.5254698918
191.624246777790.06985502455131.271478653240.6252020472891.240443615083.18632596079-0.0391525123509-0.03207692120450.1050695346990.0187021650417-0.1942299376340.0831584231532-0.0296005947651-0.05925198785450.1108282609530.195934861662-0.00976919639540.01226993878570.204498474240.01175657246390.203327735218-31.8929600381-1.03441948661.2805562487
204.34800988025-1.6899615278-0.6885636404010.703482429680.5921217118022.010612578320.3674552640370.2205502505150.00793655851359-0.0989276262141-0.226378457681-0.0067360596804-0.1340029467490.0147491747744-0.03116389646550.23289560563-0.0264595603605-0.001574896923190.1571108944160.0192428704620.230922946694-19.2763508927-13.683970534942.0628705105
211.353275672860.55318422514-0.9318852371111.800627152340.2511011928221.74859112172-0.09879257966340.0140748918821-0.03417352789020.04210237273590.191805054568-0.2936251212550.2531033233820.190777137469-0.007277214329340.2430767865260.0639729318415-0.004236241911270.277660174826-0.0443121875140.1996506035826.53005687861-8.26667241057-8.18285893301
221.80357381955-0.4417889096630.5728366065886.70054143837-0.9076391823421.480529222250.239893535262-0.3412996472080.3997525932420.0208778306623-0.3019344682410.2526170537420.03366896511250.6314192707080.4844032308140.239342463142-0.07900141865170.04465995410.408912508943-0.0594974046390.3071396820779.019849997411.353531055448.63335029365
230.409473032282-0.0073912453885-0.2104473761811.44560038093-0.1816045568590.189917867483-0.0955283874725-0.2274241206690.2357133102130.1249104547570.1892365698070.3013987121930.09237374323980.0537229719573-0.081828452430.2773297865420.0713733897342-0.02093547954660.357752387302-0.04888293038430.273621631917-5.89145921527-5.216180081252.74990482062
240.31783026699-0.3192902376460.1954883692582.33531218649-0.08886273482713.31102413501-0.172154476855-0.0278665696110.09594648895320.3798556221390.214469597637-0.0301285439170.2515488523210.07893528800110.0001521311125380.4176562532640.07182586801140.01429784784480.3487749818050.01916539144590.332785952691-12.6430696033-16.444126093112.8524439418
251.153976508831.32165372705-0.9429295670454.21708871161-0.8855440035870.9191473844790.02521098963780.05215454745190.125043846448-0.2268131058940.0914339075585-0.1423730318360.0113000825650.0536548926717-0.08260599674770.214875362140.00469043719037-0.02964055263370.201332853951-0.01768181388750.158413138612-6.09594858554-4.54048579429-9.38409536286
261.430102538021.619908344360.02432792995391.88198275827-0.4690181909961.374505742120.215845105616-0.219584557271-0.006636819277270.156324961439-0.034974101143-0.1739208316240.1023043195910.0458635692606-0.03342041865120.2360695131070.0127726358972-0.03102321437440.319956463254-0.05071816471870.259077888830.9407373103-22.997942746649.6416566984
271.209560282370.946284650581-0.7261074812811.20696296625-0.8142354202491.100460695350.394118683002-0.0117014719673-0.02256166034250.08826038765270.1608262805950.0893238965580.1819202753070.3768819128781.43775205960.304903355330.0623003248429-0.1080055855550.377303785291-0.1393724153410.27066724012528.417777421-33.599398770633.925489483
281.488015844760.140840714576-0.4256135024171.59766077177-0.4797412439990.9502090407150.2513432201770.315475624733-0.5093845379880.105435311065-0.08702277144460.003498078451430.1419249131090.169307139535-0.1388096928060.3182841682570.106705231002-0.1082765238510.392648760029-0.1442334344050.48530891273937.8364008718-41.603574810329.6504460686
294.175322102930.272421963707-1.299266590911.69008083879-0.1496694176282.165693713820.3202660036520.108242419084-0.0599619746102-0.165335601289-0.1560300410890.0980461250791-0.2816456182360.187863076329-0.1653622527810.242350299790.01428428166980.02548085552580.22590600476-0.033622380520.2427648616925.7198789017-19.845861742136.8626124841
303.0943424425-1.05320769448-1.192634219211.83824999253-0.006556280569470.8460534145120.06909911004240.0332519213294-0.294342537248-0.183522944897-0.0757357239637-0.0349808724215-0.0943303494793-0.0836790464396-0.05860588632070.2505818242110.01138372848650.03522799386640.274466000506-0.044144655030.24494707411234.55659335739.463658278151.53024049481
311.841570088590.0630679417532-6.14500979221E-52.87080440241-0.1256890938471.117819704130.1471562543790.2944396983640.0441746032483-0.5326809224890.00711204987083-0.172599244235-0.238488322750.0709716459893-0.08949571215240.3459960940890.0472625883080.03350659392280.3955316261270.03160668018210.26233984371128.144951657422.8386560569-4.42094789844
323.385495355170.3019687844270.5121329271140.457409270924-0.589469568690.961502403363-0.0834943811091-0.4081972332280.1685488225610.0547097526208-0.0459520044732-0.0432539466155-0.140984402479-0.4046464877940.09337155412850.2569438672750.03142964861430.03578813036740.238100201409-0.02256467915630.21947487421528.871706695226.842749764514.2029707411
332.62115338994-1.862122882770.3787291087754.108799967460.06038714699010.4154034491430.101770426814-0.1658798328740.185490429457-0.0524804554094-0.0187910559785-0.264040452664-0.111495401688-0.017123583379-0.06739132275790.24576195472-0.006718015308440.05890931928090.2945007321670.006072530607460.23913370301338.42979883834.824125711718.4657081017
345.011577338130.7862778133161.455533746511.819786126230.06944453118960.4241187935040.1814212879980.0984674968182-0.2348168273670.0025199455877-0.142692469327-0.0348202913470.2217823081360.0345162110268-0.09554228601250.2790112028980.005071608873260.03269591546510.279633635863-0.005966424401040.20230024291126.151646619713.178959577311.2533889104
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 123 )
2X-RAY DIFFRACTION2chain 'A' and (resid 124 through 217 )
3X-RAY DIFFRACTION3chain 'A' and (resid 218 through 263 )
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 93 )
5X-RAY DIFFRACTION5chain 'B' and (resid 94 through 116 )
6X-RAY DIFFRACTION6chain 'B' and (resid 117 through 217 )
7X-RAY DIFFRACTION7chain 'B' and (resid 218 through 261 )
8X-RAY DIFFRACTION8chain 'C' and (resid 4 through 123 )
9X-RAY DIFFRACTION9chain 'C' and (resid 124 through 217 )
10X-RAY DIFFRACTION10chain 'C' and (resid 218 through 262 )
11X-RAY DIFFRACTION11chain 'D' and (resid 3 through 65 )
12X-RAY DIFFRACTION12chain 'D' and (resid 66 through 93 )
13X-RAY DIFFRACTION13chain 'D' and (resid 94 through 123 )
14X-RAY DIFFRACTION14chain 'D' and (resid 124 through 217 )
15X-RAY DIFFRACTION15chain 'D' and (resid 218 through 261 )
16X-RAY DIFFRACTION16chain 'E' and (resid 4 through 65 )
17X-RAY DIFFRACTION17chain 'E' and (resid 66 through 93 )
18X-RAY DIFFRACTION18chain 'E' and (resid 94 through 123 )
19X-RAY DIFFRACTION19chain 'E' and (resid 124 through 217 )
20X-RAY DIFFRACTION20chain 'E' and (resid 218 through 261 )
21X-RAY DIFFRACTION21chain 'F' and (resid 4 through 65 )
22X-RAY DIFFRACTION22chain 'F' and (resid 66 through 79 )
23X-RAY DIFFRACTION23chain 'F' and (resid 80 through 123 )
24X-RAY DIFFRACTION24chain 'F' and (resid 124 through 217 )
25X-RAY DIFFRACTION25chain 'F' and (resid 218 through 261 )
26X-RAY DIFFRACTION26chain 'G' and (resid 4 through 93 )
27X-RAY DIFFRACTION27chain 'G' and (resid 94 through 123 )
28X-RAY DIFFRACTION28chain 'G' and (resid 124 through 217 )
29X-RAY DIFFRACTION29chain 'G' and (resid 218 through 263 )
30X-RAY DIFFRACTION30chain 'H' and (resid 4 through 47 )
31X-RAY DIFFRACTION31chain 'H' and (resid 48 through 93 )
32X-RAY DIFFRACTION32chain 'H' and (resid 94 through 123 )
33X-RAY DIFFRACTION33chain 'H' and (resid 124 through 217 )
34X-RAY DIFFRACTION34chain 'H' and (resid 218 through 263 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more