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- PDB-5x1v: PKM2 in complex with compound 2 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5x1v
TitlePKM2 in complex with compound 2
ComponentsPyruvate kinase PKM
KeywordsTRANSFERASE / activator / complex
Function / homology
Function and homology information


programmed cell death / pyruvate kinase / pyruvate kinase activity / positive regulation of cytoplasmic translation / histone H3T11 kinase activity / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum ...programmed cell death / pyruvate kinase / pyruvate kinase activity / positive regulation of cytoplasmic translation / histone H3T11 kinase activity / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum / glycolytic process / non-specific protein-tyrosine kinase / cilium / cellular response to insulin stimulus / extracellular vesicle / MHC class II protein complex binding / collagen-containing extracellular matrix / protein tyrosine kinase activity / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / transcription coactivator activity / non-specific serine/threonine protein kinase / cadherin binding / phosphorylation / mRNA binding / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / RNA binding / extracellular exosome / extracellular region / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily ...Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-7XX / 1,6-di-O-phosphono-beta-D-fructofuranose / Pyruvate kinase PKM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMatsui, Y. / Hanzawa, H.
CitationJournal: Bioorg. Med. Chem. / Year: 2017
Title: Discovery and structure-guided fragment-linking of 4-(2,3-dichlorobenzoyl)-1-methyl-pyrrole-2-carboxamide as a pyruvate kinase M2 activator
Authors: Matsui, Y. / Yasumatsu, I. / Asahi, T. / Kitamura, T. / Kanai, K. / Ubukata, O. / Hayasaka, H. / Takaishi, S. / Hanzawa, H. / Katakura, S.
History
DepositionJan 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate kinase PKM
B: Pyruvate kinase PKM
C: Pyruvate kinase PKM
D: Pyruvate kinase PKM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,74912
Polymers240,2004
Non-polymers2,5498
Water8,521473
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20340 Å2
ΔGint-108.9 kcal/mol
Surface area71600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.468, 151.658, 92.079
Angle α, β, γ (deg.)90.00, 102.44, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D
13A
23B
33C
43D
14A
24B
34C
44D

NCS domain segments:

Refine code: 5

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRARGARGAA15 - 4334 - 62
211THRTHRARGARGBB15 - 4334 - 62
311THRTHRARGARGCC15 - 4334 - 62
411THRTHRARGARGDD15 - 4334 - 62
112THRTHRPHEPHEAA45 - 7664 - 95
212THRTHRPHEPHEBB45 - 7664 - 95
312THRTHRPHEPHECC45 - 7664 - 95
412THRTHRPHEPHEDD45 - 7664 - 95
122HISHISSERSERAA84 - 97103 - 116
222HISHISSERSERBB84 - 97103 - 116
322HISHISSERSERCC84 - 97103 - 116
422HISHISSERSERDD84 - 97103 - 116
132ARGARGTHRTHRAA106 - 114125 - 133
232ARGARGTHRTHRBB106 - 114125 - 133
332ARGARGTHRTHRCC106 - 114125 - 133
432ARGARGTHRTHRDD106 - 114125 - 133
142ASPASPLYSLYSAA238 - 247257 - 266
242ASPASPLYSLYSBB238 - 247257 - 266
342ASPASPLYSLYSCC238 - 247257 - 266
442ASPASPLYSLYSDD238 - 247257 - 266
152ASNASNLEULEUAA264 - 297283 - 316
252ASNASNLEULEUBB264 - 297283 - 316
352ASNASNLEULEUCC264 - 297283 - 316
452ASNASNLEULEUDD264 - 297283 - 316
162LYSLYSILEILEAA305 - 389324 - 408
262LYSLYSILEILEBB305 - 389324 - 408
362LYSLYSILEILECC305 - 389324 - 408
462LYSLYSILEILEDD305 - 389324 - 408
113ILEILEILEILEAA156 - 164175 - 183
213ILEILEILEILEBB156 - 164175 - 183
313ILEILEILEILECC156 - 164175 - 183
413ILEILEILEILEDD156 - 164175 - 183
123SERSERLYSLYSAA172 - 186191 - 205
223SERSERLYSLYSBB172 - 186191 - 205
323SERSERLYSLYSCC172 - 186191 - 205
423SERSERLYSLYSDD172 - 186191 - 205
133LEULEULEULEUAA203 - 211222 - 230
233LEULEULEULEUBB203 - 211222 - 230
333LEULEULEULEUCC203 - 211222 - 230
433LEULEULEULEUDD203 - 211222 - 230
114GLUGLULEULEUAA410 - 473429 - 492
214GLUGLULEULEUBB410 - 473429 - 492
314GLUGLULEULEUCC410 - 473429 - 492
414GLUGLULEULEUDD410 - 473429 - 492
124ARGARGPROPROAA489 - 531508 - 550
224ARGARGPROPROBB489 - 531508 - 550
324ARGARGPROPROCC489 - 531508 - 550
424ARGARGPROPRODD489 - 531508 - 550

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(1, 1), (1, 1), (1)1
2given(2, -0.759593, -0.422644), (2, -0.427728, -0.247985), (2, 0.489966, -0.871708)0.494358, -0.869225, 0.00759
3given(3, 0.112255, 0.952162), (3, 0.952932, -0.184225), (3, 0.281638, 0.243821)0.284229, 0.240794, -0.928026
4given(4, -0.356395, -0.520749), (4, -0.522923, -0.576892), (4, -0.774296, 0.629298)-0.77576, 0.627492, -0.06671
5given(1, 1), (1, 1), (1)1
6given(2, -0.770785, -0.431626), (2, -0.397727, -0.248598), (2, 0.497699, -0.867121)0.468604, -0.883183, 0.019946
7given(3, 0.121477, 0.942462), (3, 0.951703, -0.199727), (3, 0.281967, 0.268094)0.311463, 0.233176, -0.921206
8given(4, -0.35824, -0.534687), (4, -0.529159, -0.559101), (4, -0.769191, 0.633652)-0.765359, 0.638276, -0.082643
9given(1, 1), (1, 1), (1)1
10given(2, -0.778655, -0.343207), (2, -0.251245, -0.596555), (2, 0.574954, -0.725486)0.525267, -0.762232, 0.378282
11given(3, 0.144644, 0.95828), (3, 0.968095, -0.188578), (3, 0.204622, 0.214796)0.24653, 0.165017, -0.954983
12given(4, -0.29193, -0.521126), (4, -0.807076, -0.315736), (4, -0.51323, 0.79293)-0.802, 0.498938, -0.328415
13given(1, 1), (1, 1), (1)1
14given(2, -0.750348, -0.461471), (2, -0.414095, -0.229981), (2, 0.51527, -0.856827)0.473311, -0.880701, -0.018528
15given(3, 0.149613, 0.950561), (3, 0.960421, -0.205116), (3, 0.234961, 0.233153)0.272119, 0.188462, -0.943628
16given(4, -0.377327, -0.517033), (4, -0.514504, -0.572779), (4, -0.770006, 0.636083)-0.76831, 0.63813, -0.049891

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Components

#1: Protein
Pyruvate kinase PKM / Cytosolic thyroid hormone-binding protein / CTHBP / Opa-interacting protein 3 / OIP-3 / Pyruvate ...Cytosolic thyroid hormone-binding protein / CTHBP / Opa-interacting protein 3 / OIP-3 / Pyruvate kinase 2/3 / Pyruvate kinase muscle isozyme / Thyroid hormone-binding protein 1 / THBP1 / Tumor M2-PK / p58


Mass: 60050.102 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKM, OIP3, PK2, PK3, PKM2 / Production host: Escherichia coli (E. coli) / References: UniProt: P14618, pyruvate kinase
#2: Sugar
ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose / Fructose 1,6-bisphosphate


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-7XX / 4-[2,3-bis(chloranyl)phenyl]carbonyl-1-methyl-pyrrole-2-carboxamide


Mass: 297.137 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H10Cl2N2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 473 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: PEG 3350, tryptone, MES

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 122943 / % possible obs: 98.3 % / Redundancy: 3 % / Rsym value: 0.062 / Net I/σ(I): 20.7
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3 / Num. unique obs: 6260 / Rsym value: 0.291 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house structure

Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / SU B: 15.34 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.308 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27381 12248 10 %RANDOM
Rwork0.23362 ---
obs0.2376 110648 97.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.705 Å2
Baniso -1Baniso -2Baniso -3
1--2.73 Å20 Å2-3.86 Å2
2---1.92 Å2-0 Å2
3---5.01 Å2
Refinement stepCycle: 1 / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15738 0 156 473 16367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01916150
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.98221845
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38352047
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26523.94665
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.448152896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.83715124
X-RAY DIFFRACTIONr_chiral_restr0.1080.22507
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112049
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A116MEDIUM POSITIONAL0.130.5
12B116MEDIUM POSITIONAL0.110.5
13C116MEDIUM POSITIONAL0.080.5
14D116MEDIUM POSITIONAL0.10.5
11A111LOOSE POSITIONAL0.375
12B111LOOSE POSITIONAL0.335
13C111LOOSE POSITIONAL0.375
14D111LOOSE POSITIONAL0.315
11A116MEDIUM THERMAL8.212
12B116MEDIUM THERMAL7.182
13C116MEDIUM THERMAL1.822
14D116MEDIUM THERMAL1.962
11A111LOOSE THERMAL8.210
12B111LOOSE THERMAL7.3510
13C111LOOSE THERMAL2.1310
14D111LOOSE THERMAL2.6510
21A736MEDIUM POSITIONAL0.150.5
22B736MEDIUM POSITIONAL0.130.5
23C736MEDIUM POSITIONAL0.150.5
24D736MEDIUM POSITIONAL0.10.5
21A661LOOSE POSITIONAL0.585
22B661LOOSE POSITIONAL0.465
23C661LOOSE POSITIONAL0.545
24D661LOOSE POSITIONAL0.485
21A736MEDIUM THERMAL4.692
22B736MEDIUM THERMAL3.132
23C736MEDIUM THERMAL2.512
24D736MEDIUM THERMAL1.912
21A661LOOSE THERMAL5.1110
22B661LOOSE THERMAL3.4810
23C661LOOSE THERMAL3.3610
24D661LOOSE THERMAL2.3710
31A132MEDIUM POSITIONAL0.210.5
32B132MEDIUM POSITIONAL0.180.5
33C132MEDIUM POSITIONAL0.20.5
34D132MEDIUM POSITIONAL0.220.5
31A131LOOSE POSITIONAL0.615
32B131LOOSE POSITIONAL0.715
33C131LOOSE POSITIONAL0.565
34D131LOOSE POSITIONAL0.645
31A132MEDIUM THERMAL13.32
32B132MEDIUM THERMAL2.82
33C132MEDIUM THERMAL19.742
34D132MEDIUM THERMAL9.192
31A131LOOSE THERMAL14.0510
32B131LOOSE THERMAL3.7910
33C131LOOSE THERMAL19.8610
34D131LOOSE THERMAL8.4310
41A428MEDIUM POSITIONAL0.130.5
42B428MEDIUM POSITIONAL0.140.5
43C428MEDIUM POSITIONAL0.160.5
44D428MEDIUM POSITIONAL0.130.5
41A387LOOSE POSITIONAL0.635
42B387LOOSE POSITIONAL0.535
43C387LOOSE POSITIONAL0.685
44D387LOOSE POSITIONAL0.545
41A428MEDIUM THERMAL7.272
42B428MEDIUM THERMAL5.622
43C428MEDIUM THERMAL3.182
44D428MEDIUM THERMAL4.192
41A387LOOSE THERMAL6.9410
42B387LOOSE THERMAL5.3710
43C387LOOSE THERMAL3.4810
44D387LOOSE THERMAL4.3310
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 873 -
Rwork0.348 7864 -
obs--96.01 %
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)
10.22870.07970.14110.1426-0.05970.20810.01540.0786-0.00450.0009-0.0158-0.0281-0.00680.0310.00040.12950.02680.10490.25530.03940.091923.074919.42515.8915
20.65520.10570.56370.4349-0.18510.6758-0.01030.2362-0.1109-0.11070.1293-0.00190.02260.1234-0.1190.24490.05870.04870.3342-0.0510.038112.58966.818-29.7649
30.1915-0.07880.12320.1856-0.03670.11150.0096-0.0182-0.0268-0.0539-0.0310.05570.00480.02340.02140.18120.01820.03070.1269-0.02760.121410.9962-33.558230.9821
40.25130.09470.02291.0632-0.1422.49380.00060.03030.0001-0.0692-0.0956-0.08650.04940.15670.09510.12370.03880.11840.16860.0290.115746.2708-44.666439.4207
50.17310.0392-0.03460.3236-0.04490.01240.03250.00520.00150.0341-0.0425-0.0455-0.0007-0.0050.010.186-0.00570.02330.15040.00790.089333.5168-4.87145.2159
60.10160.3502-0.08671.67250.2731.08510.0598-0.05980.02650.2297-0.12620.180.0502-0.01750.06630.2147-0.05020.10240.14670.00220.109810.301-21.691371.4963
70.1476-0.08960.06090.333-0.1060.07850.11140.0522-0.0393-0.0471-0.02210.07620.01390.0229-0.08930.1250.04010.01970.23350.00260.1095-10.9908-0.02795.4913
80.2012-0.2461-0.21392.8882-1.4291.9469-0.0495-0.01730.13440.01430.0681-0.0071-0.0314-0.0697-0.01860.06940.0434-0.02410.15570.03550.2456-14.359536.35443.2492
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B14 - 116
2X-RAY DIFFRACTION1B219 - 531
3X-RAY DIFFRACTION2B117 - 218
4X-RAY DIFFRACTION3C14 - 116
5X-RAY DIFFRACTION3C219 - 531
6X-RAY DIFFRACTION4C117 - 218
7X-RAY DIFFRACTION5D14 - 116
8X-RAY DIFFRACTION5D219 - 531
9X-RAY DIFFRACTION6D117 - 218
10X-RAY DIFFRACTION7A14 - 116
11X-RAY DIFFRACTION7A219 - 531
12X-RAY DIFFRACTION8A117 - 218

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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

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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

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