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- PDB-2w8f: Aplysia californica AChBP bound to in silico compound 31 -

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Basic information

Entry
Database: PDB / ID: 2w8f
TitleAplysia californica AChBP bound to in silico compound 31
ComponentsSOLUBLE ACETYLCHOLINE RECEPTOR
KeywordsRECEPTOR / ACETYLCHOLINE RECEPTOR INHIBITOR / ACETYLCHOLINE BINDING PROTEIN / POSTSYNAPTIC NEUROTOXIN / NICOTINIC ACETYLCHOLINE RECEPTOR-TOXIN COMPLEX / NEUROTOXIN / TOXIN / AMIDATION / CONOTOXIN
Function / homology
Function and homology information


acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / response to nicotine / neuron projection / synapse / identical protein binding / membrane / metal ion binding
Similarity search - Function
Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-BS1 / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsUlens, C. / Akdemir, A. / Jongejan, A. / van Elk, R. / Edink, E. / Bertrand, S. / Perrakis, A. / Leurs, R. / Smit, A.B. / Sixma, T.K. ...Ulens, C. / Akdemir, A. / Jongejan, A. / van Elk, R. / Edink, E. / Bertrand, S. / Perrakis, A. / Leurs, R. / Smit, A.B. / Sixma, T.K. / Bertrand, D. / de Esch, I.J.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Use of Acetylcholine Binding Protein in the Search for Novel Alpha7 Nicotinic Receptor Ligands. In Silico Docking, Pharmacological Screening, and X- Ray Analysis.
Authors: Ulens, C. / Akdemir, A. / Jongejan, A. / Van Elk, R. / Bertrand, S. / Perrakis, A. / Leurs, R. / Smit, A.B. / Sixma, T.K. / Bertrand, D. / De Esch, I.J.
History
DepositionJan 16, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Sep 28, 2011Group: Database references
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SOLUBLE ACETYLCHOLINE RECEPTOR
B: SOLUBLE ACETYLCHOLINE RECEPTOR
C: SOLUBLE ACETYLCHOLINE RECEPTOR
D: SOLUBLE ACETYLCHOLINE RECEPTOR
E: SOLUBLE ACETYLCHOLINE RECEPTOR
F: SOLUBLE ACETYLCHOLINE RECEPTOR
G: SOLUBLE ACETYLCHOLINE RECEPTOR
H: SOLUBLE ACETYLCHOLINE RECEPTOR
I: SOLUBLE ACETYLCHOLINE RECEPTOR
J: SOLUBLE ACETYLCHOLINE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,58312
Polymers246,88610
Non-polymers6972
Water1,26170
1
A: SOLUBLE ACETYLCHOLINE RECEPTOR
B: SOLUBLE ACETYLCHOLINE RECEPTOR
C: SOLUBLE ACETYLCHOLINE RECEPTOR
D: SOLUBLE ACETYLCHOLINE RECEPTOR
E: SOLUBLE ACETYLCHOLINE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,7916
Polymers123,4435
Non-polymers3491
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12400 Å2
ΔGint-63.5 kcal/mol
Surface area43670 Å2
MethodPISA
2
F: SOLUBLE ACETYLCHOLINE RECEPTOR
G: SOLUBLE ACETYLCHOLINE RECEPTOR
H: SOLUBLE ACETYLCHOLINE RECEPTOR
I: SOLUBLE ACETYLCHOLINE RECEPTOR
J: SOLUBLE ACETYLCHOLINE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,7916
Polymers123,4435
Non-polymers3491
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12430 Å2
ΔGint-65 kcal/mol
Surface area43820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.800, 76.800, 725.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNVALVAL1AA1 - 391 - 39
21GLNGLNVALVAL1BB1 - 391 - 39
31GLNGLNVALVAL1CC1 - 391 - 39
41GLNGLNVALVAL1DD1 - 391 - 39
51GLNGLNVALVAL1EE1 - 391 - 39
61GLNGLNVALVAL1FF1 - 391 - 39
71GLNGLNVALVAL1GG1 - 391 - 39
81GLNGLNVALVAL1HH1 - 391 - 39
91GLNGLNVALVAL1II1 - 391 - 39
101GLNGLNVALVAL1JJ1 - 391 - 39
12LYSLYSVALVAL6AA40 - 4840 - 48
22LYSLYSVALVAL6BB40 - 4840 - 48
32LYSLYSVALVAL6CC40 - 4840 - 48
42LYSLYSVALVAL6DD40 - 4840 - 48
52LYSLYSVALVAL6EE40 - 4840 - 48
62LYSLYSVALVAL6FF40 - 4840 - 48
72LYSLYSVALVAL6GG40 - 4840 - 48
82LYSLYSVALVAL6HH40 - 4840 - 48
92LYSLYSVALVAL6II40 - 4840 - 48
102LYSLYSVALVAL6JJ40 - 4840 - 48
13ASPASPASPASP1AA49 - 13149 - 131
23ASPASPASPASP1BB49 - 13149 - 131
33ASPASPASPASP1CC49 - 13149 - 131
43ASPASPASPASP1DD49 - 13149 - 131
53ASPASPASPASP1EE49 - 13149 - 131
63ASPASPASPASP1FF49 - 13149 - 131
73ASPASPASPASP1GG49 - 13149 - 131
83ASPASPASPASP1HH49 - 13149 - 131
93ASPASPASPASP1II49 - 13149 - 131
103ASPASPASPASP1JJ49 - 13149 - 131
14SERSERGLYGLY6AA132 - 143132 - 143
24SERSERGLYGLY6BB132 - 143132 - 143
34SERSERGLYGLY6CC132 - 143132 - 143
44SERSERGLYGLY6DD132 - 143132 - 143
54SERSERGLYGLY6EE132 - 143132 - 143
64SERSERGLYGLY6FF132 - 143132 - 143
74SERSERGLYGLY6GG132 - 143132 - 143
84SERSERGLYGLY6HH132 - 143132 - 143
94SERSERGLYGLY6II132 - 143132 - 143
104SERSERGLYGLY6JJ132 - 143132 - 143
15SERSERARGARG1AA144 - 181144 - 181
25SERSERARGARG1BB144 - 181144 - 181
35SERSERARGARG1CC144 - 181144 - 181
45SERSERARGARG1DD144 - 181144 - 181
55SERSERARGARG1EE144 - 181144 - 181
65SERSERARGARG1FF144 - 181144 - 181
75SERSERARGARG1GG144 - 181144 - 181
85SERSERARGARG1HH144 - 181144 - 181
95SERSERARGARG1II144 - 181144 - 181
105SERSERARGARG1JJ144 - 181144 - 181
16GLNGLNASPASP6AA182 - 195182 - 195
26GLNGLNASPASP6BB182 - 195182 - 195
36GLNGLNASPASP6CC182 - 195182 - 195
46GLNGLNASPASP6DD182 - 195182 - 195
56GLNGLNASPASP6EE182 - 195182 - 195
66GLNGLNASPASP6FF182 - 195182 - 195
76GLNGLNASPASP6GG182 - 195182 - 195
86GLNGLNASPASP6HH182 - 195182 - 195
96GLNGLNASPASP6II182 - 195182 - 195
106GLNGLNASPASP6JJ182 - 195182 - 195
17VALVALARGARG1AA196 - 205196 - 205
27VALVALARGARG1BB196 - 205196 - 205
37VALVALARGARG1CC196 - 205196 - 205
47VALVALARGARG1DD196 - 205196 - 205
57VALVALARGARG1EE196 - 205196 - 205
67VALVALARGARG1FF196 - 205196 - 205
77VALVALARGARG1GG196 - 205196 - 205
87VALVALARGARG1HH196 - 205196 - 205
97VALVALARGARG1II196 - 205196 - 205
107VALVALARGARG1JJ196 - 205196 - 205

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Components

#1: Protein
SOLUBLE ACETYLCHOLINE RECEPTOR


Mass: 24688.578 Da / Num. of mol.: 10 / Fragment: RESIDUES 20-236 / Source method: isolated from a natural source / Source: (natural) APLYSIA CALIFORNICA (California sea hare) / References: UniProt: Q8WSF8
#2: Chemical ChemComp-BS1 / (3-EXO)-3-(10,11-DIHYDRO-5H-DIBENZO[A,D][7]ANNULEN-5-YLOXY)-8,8-DIMETHYL-8-AZONIABICYCLO[3.2.1]OCTANE


Mass: 348.501 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H30NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCOMPOUND 31 IS 3ALPHA-[(10,11-DIHYDRO-5H-DIBENZO[A,D] CYCLOHEPTEN-5-YL)OXY]-8,8-DIMETHYL-8- ...COMPOUND 31 IS 3ALPHA-[(10,11-DIHYDRO-5H-DIBENZO[A,D] CYCLOHEPTEN-5-YL)OXY]-8,8-DIMETHYL-8-AZONIABICYCLO[3.2.1] OCTANE

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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: 2.7 Å3/Da / Density % sol: 53.7 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0 Å / Relative weight: 1
ReflectionResolution: 2.7→44.6 Å / Num. obs: 67908 / % possible obs: 98 % / Observed criterion σ(I): 1 / Redundancy: 8.8 % / Rsym value: 0.077 / Net I/σ(I): 9.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.49 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
EVAL15data reduction
EVAL15data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C9T
Resolution: 2.7→42.76 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.91 / SU B: 37.757 / SU ML: 0.338 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 3549 5.1 %RANDOM
Rwork0.237 ---
obs0.239 65580 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.65 Å2
Baniso -1Baniso -2Baniso -3
1-2.93 Å21.47 Å20 Å2
2--2.93 Å20 Å2
3----4.4 Å2
Refinement stepCycle: LAST / Resolution: 2.7→42.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16360 0 52 70 16482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02216840
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.95623000
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.91752040
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.98424.557790
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.454152720
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5961590
X-RAY DIFFRACTIONr_chiral_restr0.0930.22580
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212882
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.26765
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3240.211713
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2574
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4690.2111
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5120.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5721.510508
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.757216850
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.18837276
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9484.56150
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1369tight positional0.070.05
2B1369tight positional0.070.05
3C1369tight positional0.060.05
4D1369tight positional0.060.05
5E1369tight positional0.060.05
6F1369tight positional0.070.05
7G1369tight positional0.060.05
8H1369tight positional0.070.05
9I1369tight positional0.070.05
10J1369tight positional0.080.05
1A267loose positional0.655
2B267loose positional0.85
3C267loose positional1.285
4D267loose positional0.745
5E267loose positional0.615
6F267loose positional0.635
7G267loose positional0.75
8H267loose positional0.865
9I267loose positional0.685
10J267loose positional0.685
1A1369tight thermal0.130.5
2B1369tight thermal0.120.5
3C1369tight thermal0.10.5
4D1369tight thermal0.10.5
5E1369tight thermal0.10.5
6F1369tight thermal0.130.5
7G1369tight thermal0.120.5
8H1369tight thermal0.140.5
9I1369tight thermal0.120.5
10J1369tight thermal0.10.5
1A267loose thermal3.910
2B267loose thermal4.0310
3C267loose thermal3.7110
4D267loose thermal4.8210
5E267loose thermal2.7410
6F267loose thermal5.1410
7G267loose thermal2.3410
8H267loose thermal5.7510
9I267loose thermal2.1410
10J267loose thermal3.6910
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 244 -
Rwork0.398 4265 -
obs--87.5 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.44390.5440.82051.4782-0.16883.26540.1381-0.25360.03870.1196-0.13570.0347-0.12590.2684-0.0024-0.48660.01310.0816-0.0817-0.0887-0.260555.594148.465849.1429
22.47670.04340.36073.1606-0.30172.73970.1691-0.2596-0.26270.1879-0.05650.08960.3984-0.0112-0.1126-0.43570.02130.0747-0.1187-0.0424-0.224242.288225.314847.3491
32.8628-0.3071-0.15622.9745-0.23873.55160.06540.1546-0.5571-0.1629-0.0136-0.01080.87180.2042-0.0517-0.20570.1069-0.0715-0.094-0.1665-0.107845.33916.354622.3431
43.6272-0.4278-0.15453.52620.30292.67740.00190.5094-0.1291-0.47-0.0202-0.30750.16460.39690.0183-0.27640.16920.050.1774-0.0279-0.319960.369233.88728.8173
54.9894-0.4169-0.41952.47860.35443.47230.04460.09150.4901-0.1670.0293-0.3283-0.31690.7652-0.0739-0.3851-0.06660.06720.01720.0152-0.19466.764753.869925.4506
63.3491-0.2215-0.3291.71020.71673.85660.26990.2459-0.013-0.179-0.20230.0819-0.4335-0.0397-0.0675-0.4338-0.07110.1095-0.08060.0534-0.372317.148753.200168.2447
74.20611.0352-0.57992.80270.41894.3959-0.1627-0.6447-0.7487-0.1313-0.181-0.1770.82280.70870.3437-0.47930.10620.1440.18510.2024-0.113330.085833.350680.4648
82.77720.7648-1.90813.7136-0.21524.5289-0.1812-0.8682-0.45290.2527-0.0417-0.10880.75761.55690.2229-0.64560.0085-0.01410.9560.3495-0.160427.109636.7583106.8624
93.7571-0.1308-2.3542.9064-0.04145.3410.3132-0.88840.10580.2438-0.00290.0516-0.80121.056-0.3103-0.3638-0.45040.02760.2658-0.0398-0.327112.419458.7107110.7663
106.02090.8887-2.81562.6159-0.42136.09260.8180.3920.7552-0.0448-0.22080.3847-1.651-0.6478-0.59720.08390.03270.2445-0.17690.0179-0.1456.198369.004786.8586
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 205
2X-RAY DIFFRACTION2B1 - 205
3X-RAY DIFFRACTION3C1 - 205
4X-RAY DIFFRACTION4D1 - 205
5X-RAY DIFFRACTION5E1 - 205
6X-RAY DIFFRACTION6F1 - 205
7X-RAY DIFFRACTION7G1 - 205
8X-RAY DIFFRACTION8H1 - 205
9X-RAY DIFFRACTION9I1 - 205
10X-RAY DIFFRACTION10J1 - 205

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