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- PDB-7lv3: Crystal structure of human protein kinase G (PKG) R-C complex in ... -

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Basic information

Entry
Database: PDB / ID: 7lv3
TitleCrystal structure of human protein kinase G (PKG) R-C complex in inhibited state
ComponentsIsoform Beta of cGMP-dependent protein kinase 1
KeywordsTRANSFERASE/INHIBITOR / Protein Kinase G / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


negative regulation of glutamate secretion / negative regulation of inositol phosphate biosynthetic process / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / cell growth involved in cardiac muscle cell development / regulation of testosterone biosynthetic process / collateral sprouting / negative regulation of platelet aggregation / positive regulation of circadian rhythm / relaxation of vascular associated smooth muscle ...negative regulation of glutamate secretion / negative regulation of inositol phosphate biosynthetic process / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / cell growth involved in cardiac muscle cell development / regulation of testosterone biosynthetic process / collateral sprouting / negative regulation of platelet aggregation / positive regulation of circadian rhythm / relaxation of vascular associated smooth muscle / Rap1 signalling / regulation of GTPase activity / cGMP-mediated signaling / mitogen-activated protein kinase p38 binding / spermatid development / cGMP effects / negative regulation of vascular associated smooth muscle cell migration / negative regulation of vascular associated smooth muscle cell proliferation / dendrite development / cGMP binding / forebrain development / calcium channel regulator activity / cerebellum development / acrosomal vesicle / sarcolemma / neuron migration / actin cytoskeleton organization / positive regulation of cytosolic calcium ion concentration / Ca2+ pathway / protein kinase activity / protein phosphorylation / protein serine kinase activity / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
cGMP-dependent protein kinase, N-terminal coiled-coil domain / Coiled-coil N-terminus of cGMP-dependent protein kinase / cGMP-dependent kinase / cGMP-dependent protein kinase, catalytic domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. ...cGMP-dependent protein kinase, N-terminal coiled-coil domain / Coiled-coil N-terminus of cGMP-dependent protein kinase / cGMP-dependent kinase / cGMP-dependent protein kinase, catalytic domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Extension to Ser/Thr-type protein kinases / Jelly Rolls / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / RmlC-like jelly roll fold / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Jelly Rolls / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / cGMP-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsSharma, R. / Lying, Q. / Casteel, D. / Kim, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM090161 United States
CitationJournal: Elife / Year: 2022
Title: An auto-inhibited state of protein kinase G and implications for selective activation.
Authors: Sharma, R. / Kim, J.J. / Qin, L. / Henning, P. / Akimoto, M. / VanSchouwen, B. / Kaur, G. / Sankaran, B. / MacKenzie, K.R. / Melacini, G. / Casteel, D.E. / Herberg, F.W. / Kim, C.W.
History
DepositionFeb 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform Beta of cGMP-dependent protein kinase 1
B: Isoform Beta of cGMP-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,14111
Polymers139,7232
Non-polymers1,4189
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9820 Å2
ΔGint-63 kcal/mol
Surface area52600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.832, 112.824, 150.720
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

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
11LYSLYSPROPRO(chain 'A' and (resid 75 through 84 or resid 90...AA75 - 836 - 14
12ASPASPASPASP(chain 'A' and (resid 75 through 84 or resid 90...AA9021
13PROPROSERSER(chain 'A' and (resid 75 through 84 or resid 90...AA97 - 10228 - 33
14SERSERLEULEU(chain 'A' and (resid 75 through 84 or resid 90...AA105 - 10836 - 39
15GLUGLULEULEU(chain 'A' and (resid 75 through 84 or resid 90...AA111 - 12242 - 53
16SERSERPROPRO(chain 'A' and (resid 75 through 84 or resid 90...AA125 - 13656 - 67
17TYRTYRTYRTYR(chain 'A' and (resid 75 through 84 or resid 90...AA13970
18SERSERILEILE(chain 'A' and (resid 75 through 84 or resid 90...AA143 - 14574 - 76
19GLYGLYMETMET(chain 'A' and (resid 75 through 84 or resid 90...AA149 - 15880 - 89
110GLYGLYLYSLYS(chain 'A' and (resid 75 through 84 or resid 90...AA161 - 16292 - 93
111VALVALVALVAL(chain 'A' and (resid 75 through 84 or resid 90...AA16596
112GLYGLYGLYGLY(chain 'A' and (resid 75 through 84 or resid 90...AA169100
113CYSCYSPROPRO(chain 'A' and (resid 75 through 84 or resid 90...AA173 - 177104 - 108
114VALVALTHRTHR(chain 'A' and (resid 75 through 84 or resid 90...AA180 - 195111 - 126
115LEULEUARGARG(chain 'A' and (resid 75 through 84 or resid 90...AA204 - 209135 - 140
116CYSCYSMETMET(chain 'A' and (resid 75 through 84 or resid 90...AA211 - 216142 - 147
117THRTHRPHEPHE(chain 'A' and (resid 75 through 84 or resid 90...AA219 - 230150 - 161
118SERSERPROPRO(chain 'A' and (resid 75 through 84 or resid 90...AA233 - 241164 - 172
119ILEILEVALVAL(chain 'A' and (resid 75 through 84 or resid 90...AA244 - 251175 - 182
120GLUGLUGLYGLY(chain 'A' and (resid 75 through 84 or resid 90...AA254 - 267185 - 198
121GLYGLYSERSER(chain 'A' and (resid 75 through 84 or resid 90...AA270 - 288201 - 219
122ASPASPASPASP(chain 'A' and (resid 75 through 84 or resid 90...AA292223
123PHEPHELEULEU(chain 'A' and (resid 75 through 84 or resid 90...AA295 - 299226 - 230
124GLYGLYPHEPHE(chain 'A' and (resid 75 through 84 or resid 90...AA302 - 336233 - 267
125GLUGLULYSLYS(chain 'A' and (resid 75 through 84 or resid 90...AA355 - 357286 - 288
126TYRTYRGLUGLU(chain 'A' and (resid 75 through 84 or resid 90...AA360 - 361291 - 292
127ALAALALEULEU(chain 'A' and (resid 75 through 84 or resid 90...AA364 - 370295 - 301
128SERSERGLYGLY(chain 'A' and (resid 75 through 84 or resid 90...AA373 - 384304 - 315
129GLYGLYLEULEU(chain 'A' and (resid 75 through 84 or resid 90...AA387 - 407318 - 338
130ARGARGARGARG(chain 'A' and (resid 75 through 84 or resid 90...AA410341
131ILEILEHISHIS(chain 'A' and (resid 75 through 84 or resid 90...AA412 - 420343 - 351
132SERSERTHRTHR(chain 'A' and (resid 75 through 84 or resid 90...AA423 - 442354 - 373
133ASPASPASPASP(chain 'A' and (resid 75 through 84 or resid 90...AA445376
134TYRTYRTHRTHR(chain 'A' and (resid 75 through 84 or resid 90...AA448 - 530379 - 461
135TPOTPOPROPRO(chain 'A' and (resid 75 through 84 or resid 90...AA532 - 578463 - 509
136THRTHRASNASN(chain 'A' and (resid 75 through 84 or resid 90...AA581 - 613512 - 544
137GLUGLUASPASP(chain 'A' and (resid 75 through 84 or resid 90...AA616 - 685547 - 616
138ANPANPANPANP(chain 'A' and (resid 75 through 84 or resid 90...AE803
21LYSLYSPROPRO(chain 'B' and (resid 75 through 91 or resid 97...BB75 - 836 - 14
22ASPASPASPASP(chain 'B' and (resid 75 through 91 or resid 97...BB9021
23PROPROSERSER(chain 'B' and (resid 75 through 91 or resid 97...BB97 - 10228 - 33
24SERSERLEULEU(chain 'B' and (resid 75 through 91 or resid 97...BB105 - 10836 - 39
25GLUGLULEULEU(chain 'B' and (resid 75 through 91 or resid 97...BB111 - 12242 - 53
26SERSERPROPRO(chain 'B' and (resid 75 through 91 or resid 97...BB125 - 13656 - 67
27TYRTYRTYRTYR(chain 'B' and (resid 75 through 91 or resid 97...BB13970
28SERSERILEILE(chain 'B' and (resid 75 through 91 or resid 97...BB143 - 14574 - 76
29GLYGLYMETMET(chain 'B' and (resid 75 through 91 or resid 97...BB149 - 15880 - 89
210GLYGLYLYSLYS(chain 'B' and (resid 75 through 91 or resid 97...BB161 - 16292 - 93
211VALVALVALVAL(chain 'B' and (resid 75 through 91 or resid 97...BB16596
212GLYGLYGLYGLY(chain 'B' and (resid 75 through 91 or resid 97...BB169100
213CYSCYSPROPRO(chain 'B' and (resid 75 through 91 or resid 97...BB173 - 177104 - 108
214VALVALTHRTHR(chain 'B' and (resid 75 through 91 or resid 97...BB180 - 195111 - 126
215LEULEUARGARG(chain 'B' and (resid 75 through 91 or resid 97...BB204 - 209135 - 140
216CYSCYSMETMET(chain 'B' and (resid 75 through 91 or resid 97...BB211 - 216142 - 147
217THRTHRPHEPHE(chain 'B' and (resid 75 through 91 or resid 97...BB219 - 230150 - 161
218SERSERPROPRO(chain 'B' and (resid 75 through 91 or resid 97...BB233 - 241164 - 172
219ILEILEVALVAL(chain 'B' and (resid 75 through 91 or resid 97...BB244 - 251175 - 182
220GLUGLUGLYGLY(chain 'B' and (resid 75 through 91 or resid 97...BB254 - 267185 - 198
221GLYGLYSERSER(chain 'B' and (resid 75 through 91 or resid 97...BB270 - 288201 - 219
222ASPASPASPASP(chain 'B' and (resid 75 through 91 or resid 97...BB292223
223PHEPHELEULEU(chain 'B' and (resid 75 through 91 or resid 97...BB295 - 299226 - 230
224GLYGLYPHEPHE(chain 'B' and (resid 75 through 91 or resid 97...BB302 - 336233 - 267
225ALAALAALAALA(chain 'B' and (resid 75 through 91 or resid 97...BB356 - 358287 - 289
226TYRTYRGLUGLU(chain 'B' and (resid 75 through 91 or resid 97...BB360 - 361291 - 292
227ALAALALEULEU(chain 'B' and (resid 75 through 91 or resid 97...BB364 - 370295 - 301
228SERSERGLYGLY(chain 'B' and (resid 75 through 91 or resid 97...BB373 - 384304 - 315
229GLYGLYLEULEU(chain 'B' and (resid 75 through 91 or resid 97...BB387 - 407318 - 338
230ARGARGARGARG(chain 'B' and (resid 75 through 91 or resid 97...BB410341
231ILEILEHISHIS(chain 'B' and (resid 75 through 91 or resid 97...BB412 - 420343 - 351
232SERSERTHRTHR(chain 'B' and (resid 75 through 91 or resid 97...BB423 - 442354 - 373
233ASPASPASPASP(chain 'B' and (resid 75 through 91 or resid 97...BB445376
234TYRTYRTHRTHR(chain 'B' and (resid 75 through 91 or resid 97...BB448 - 530379 - 461
235TPOTPOPROPRO(chain 'B' and (resid 75 through 91 or resid 97...BB532 - 578463 - 509
236THRTHRASNASN(chain 'B' and (resid 75 through 91 or resid 97...BB581 - 613512 - 544
237GLUGLUASPASP(chain 'B' and (resid 75 through 91 or resid 97...BB616 - 685547 - 616
238ANPANPANPANP(chain 'B' and (resid 75 through 91 or resid 97...BI803

NCS oper: (Code: givenMatrix: (-0.999862992821, -0.00464271658216, -0.015888384753), (-0.00431572040351, -0.853544078958, 0.521002763748), (-0.0159803049007, 0.520999952456, 0.853407100625)Vector: - ...NCS oper: (Code: given
Matrix: (-0.999862992821, -0.00464271658216, -0.015888384753), (-0.00431572040351, -0.853544078958, 0.521002763748), (-0.0159803049007, 0.520999952456, 0.853407100625)
Vector: -36.4786579281, 52.573469838, -14.7335605279)

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Components

#1: Protein Isoform Beta of cGMP-dependent protein kinase 1 / cGK 1 / cGK1 / cGMP-dependent protein kinase I / cGKI


Mass: 69861.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKG1, PRKG1B, PRKGR1A, PRKGR1B / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13976, cGMP-dependent protein kinase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 120 mM ethylene glycol, 100 mM Bicine (pH 8.5), 20 % w/v PEG 8,000

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 25, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.41→49.11 Å / Num. obs: 66393 / % possible obs: 99.95 % / Redundancy: 13.4 % / Biso Wilson estimate: 69.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1027 / Net I/σ(I): 20.93
Reflection shellResolution: 2.41→2.496 Å / Rmerge(I) obs: 0.1 / Num. unique obs: 6568 / CC1/2: 0.2999

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QCS, 4Z07

2qcs

4z07


Resolution: 2.41→47.38 Å / SU ML: 0.3817 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.9407
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2383 1809 2.73 %
Rwork0.1997 64563 -
obs0.2008 66372 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.98 Å2
Refinement stepCycle: LAST / Resolution: 2.41→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9227 0 78 127 9432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00549506
X-RAY DIFFRACTIONf_angle_d0.877912912
X-RAY DIFFRACTIONf_chiral_restr0.05171443
X-RAY DIFFRACTIONf_plane_restr0.00491656
X-RAY DIFFRACTIONf_dihedral_angle_d8.70691295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.480.40531370.3484917X-RAY DIFFRACTION99.82
2.48-2.550.33771370.33034897X-RAY DIFFRACTION99.94
2.55-2.630.36191380.30244924X-RAY DIFFRACTION99.98
2.63-2.720.33691370.2944863X-RAY DIFFRACTION100
2.72-2.830.33141380.27374947X-RAY DIFFRACTION100
2.83-2.960.31771380.26714926X-RAY DIFFRACTION100
2.96-3.120.31061390.25534930X-RAY DIFFRACTION100
3.12-3.310.2961370.24074927X-RAY DIFFRACTION99.98
3.31-3.570.27131400.22424978X-RAY DIFFRACTION100
3.57-3.930.24531390.19234962X-RAY DIFFRACTION100
3.93-4.50.18961400.1575007X-RAY DIFFRACTION100
4.5-5.660.19791420.1675045X-RAY DIFFRACTION100
5.66-47.380.19711470.17045240X-RAY DIFFRACTION99.87
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)
12.437054990650.0862546900470.4070126084844.16901593306-0.1670678551573.377770684310.01575704059780.4723173277830.0218786400229-0.8026808450960.0882094210204-0.508551812391-0.2615121294130.122114675327-0.0963163115310.719950868053-0.02422293608990.1864915944910.647643009642-0.1741070425270.6021695921625.8184968150658.7074719336-35.8696648907
20.2589424687590.882259108680.1034384370666.71374062183-0.04116504886680.749696222227-0.244445749505-0.0977776850526-0.287705833824-0.2201620702090.223495995366-0.758102426990.148848022309-0.120428523774-0.008554936107430.6901823265580.1288206776760.001198630521920.618171798334-0.06179069247860.84627748419721.152471793231.3510039576-16.7060919247
33.063352827320.114723630383-0.4074669738362.243725371310.248470421322.66102253615-0.03986010890670.1140962071140.443845715007-0.127354531306-0.0744192575274-0.1793714563920.08147139964350.3297581737390.1084054876580.4368917020120.0003986805212840.04609588736760.420122001340.07974221842420.501318597689-17.529078711-5.91116346687-3.61518246737
44.777071470371.498295811630.4088530621957.6941484141-0.403976543951.48153427755-0.08102345851360.3540910432080.0755724406676-0.5170235482070.276335758430.661758019749-0.068868336935-0.389674426303-0.178066687670.457007156779-0.0209510414870.0318517164080.6217667309320.03883696820440.374715892216-41.7628771921-25.788095881-13.1437367414
50.675357398736-0.646314539577-0.1620922889843.59227948539-0.1143438237060.5558519064210.0508208432270.1603215701450.344674504102-0.3211259197820.07388597096650.237546176781-0.188007474225-0.342384457631-0.1209275973320.8397014147090.078499258654-0.137261421820.8407066787890.1552300614590.718174258797-52.60639738719.21459879246-14.5287462087
64.96239710636-0.532561958239-0.7517021819362.39451355476-0.01401067290691.836319664540.002391570869670.230151532675-0.463840912893-0.368405296983-0.1427984344240.4225928246940.175314602167-0.3799122562110.103870625790.565643079842-0.0610318749793-0.02799680510290.54409821627-0.1680441333920.477165165665-18.611825731656.0945355528-20.2973566855
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 73 through 257 )
2X-RAY DIFFRACTION2chain 'A' and (resid 258 through 369 )
3X-RAY DIFFRACTION3chain 'A' and (resid 370 through 686 )
4X-RAY DIFFRACTION4chain 'B' and (resid 74 through 201 )
5X-RAY DIFFRACTION5chain 'B' and (resid 202 through 369 )
6X-RAY DIFFRACTION6chain 'B' and (resid 370 through 686 )

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  • 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

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