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- PDB-5a3u: HIF prolyl hydroxylase 2 (PHD2/EGLN1) in complex with 6-(5-oxo-4-... -

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Basic information

Entry
Database: PDB / ID: 5a3u
TitleHIF prolyl hydroxylase 2 (PHD2/EGLN1) in complex with 6-(5-oxo-4-(1H- 1,2,3-triazol-1-yl)-2,5-dihydro-1H-pyrazol-1-yl)nicotinic acid
ComponentsEGL NINE HOMOLOG 1
KeywordsOXIDOREDUCTASE / NON-HEME / IRON / 2-OXOGLUTARATE / DIOXYGENASE / HYPOXIA-INDUCIBLE FACTOR / HIF / HIF PROLYL HYDROXYLASE DOMAIN 2 / PHD2 / EGLN / OXYGENASE / HYPOXIA / DNA-BINDING / METAL-BINDING / TRANSCRIPTION / HELIX-LOOP-HELIX-BETA / DSBH / FACIAL TRIAD / ASPARAGINYL/ ASPARTYL HYDROXYLASE / TRANSCRIPTION AND EPIGENETIC REGULATION / SIGNALING / DEVELOPMENT / CELL STRUCTURE / ANKYRIN REPEAT DOMAIN / ARD / BETA-HYDROXYLATION / TRANSCRIPTION ACTIVATOR/INHIBITOR / PHOSPHORYLATION / S-NITROSYLATION
Function / homology
Function and homology information


hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline 4-dioxygenase activity / peptidyl-proline dioxygenase activity / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / negative regulation of cyclic-nucleotide phosphodiesterase activity / regulation protein catabolic process at postsynapse / intracellular oxygen homeostasis / labyrinthine layer development / 2-oxoglutarate-dependent dioxygenase activity ...hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline 4-dioxygenase activity / peptidyl-proline dioxygenase activity / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / negative regulation of cyclic-nucleotide phosphodiesterase activity / regulation protein catabolic process at postsynapse / intracellular oxygen homeostasis / labyrinthine layer development / 2-oxoglutarate-dependent dioxygenase activity / cardiac muscle tissue morphogenesis / heart trabecula formation / regulation of modification of postsynaptic structure / L-ascorbic acid binding / response to nitric oxide / ventricular septum morphogenesis / regulation of angiogenesis / ferrous iron binding / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / negative regulation of DNA-binding transcription factor activity / cellular response to hypoxia / intracellular iron ion homeostasis / postsynaptic density / response to hypoxia / intracellular membrane-bounded organelle / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleus / cytosol / cytoplasm
Similarity search - Function
Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Oxoglutarate/iron-dependent dioxygenase ...Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Chem-R8J / Egl nine homolog 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsChowdhury, R. / Gomez-Perez, V. / Schofield, C.J.
Citation
Journal: Plos One / Year: 2015
Title: Potent and Selective Triazole-Based Inhibitors of the Hypoxia-Inducible Factor Prolyl-Hydroxylases with Activity in the Murine Brain.
Authors: Chan, M.C. / Atasoylu, O. / Hodson, E. / Tumber, A. / Leung, I.K.H. / Chowdhury, R. / Gomez-Perez, V. / Demetriades, M. / Rydzik, A.M. / Holt-Martyn, J. / Tian, Y. / Bishop, T. / Claridge, T. ...Authors: Chan, M.C. / Atasoylu, O. / Hodson, E. / Tumber, A. / Leung, I.K.H. / Chowdhury, R. / Gomez-Perez, V. / Demetriades, M. / Rydzik, A.M. / Holt-Martyn, J. / Tian, Y. / Bishop, T. / Claridge, T.D.W. / Kawamura, A. / Pugh, C.W. / Ratcliffe, P.J. / Schofield, C.J.
#1: Journal: Acs Chem.Biol. / Year: 2013
Title: Selective Small Molecule Probes for the Hypoxia Inducible Factor (Hif) Prolyl Hydroxylases.
Authors: Chowdhury, R. / Candela-Lena, J.I. / Chan, M.C. / Greenald, D.J. / Yeoh, K.K. / Tian, Y. / Mcdonough, M.A. / Tumber, A. / Rose, N.R. / Conejo-Garcia, A. / Demetriades, M. / Mathavan, S. / ...Authors: Chowdhury, R. / Candela-Lena, J.I. / Chan, M.C. / Greenald, D.J. / Yeoh, K.K. / Tian, Y. / Mcdonough, M.A. / Tumber, A. / Rose, N.R. / Conejo-Garcia, A. / Demetriades, M. / Mathavan, S. / Kawamura, A. / Lee, M.K. / Van Eeden, F. / Pugh, C.W. / Ratcliffe, P.J. / Schofield, C.J.
History
DepositionJun 3, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Jan 10, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EGL NINE HOMOLOG 1
B: EGL NINE HOMOLOG 1
C: EGL NINE HOMOLOG 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2729
Polymers84,2913
Non-polymers9816
Water0
1
A: EGL NINE HOMOLOG 1
B: EGL NINE HOMOLOG 1
C: EGL NINE HOMOLOG 1
hetero molecules

A: EGL NINE HOMOLOG 1
B: EGL NINE HOMOLOG 1
C: EGL NINE HOMOLOG 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,54518
Polymers168,5826
Non-polymers1,96312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-y,-x,-z+1/31
Buried area11560 Å2
ΔGint-75.8 kcal/mol
Surface area50970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.939, 154.939, 85.401
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein EGL NINE HOMOLOG 1 / HYPOXIA-INDUCIBLE FACTOR PROLYL HYDROXYLASE 2 / HIF-PH2 / HIF-PROLYL HYDROXYLASE 2 / HPH-2 / PROLYL ...HYPOXIA-INDUCIBLE FACTOR PROLYL HYDROXYLASE 2 / HIF-PH2 / HIF-PROLYL HYDROXYLASE 2 / HPH-2 / PROLYL HYDROXYLASE DOMAIN-CONTAINING PROTEIN 2 / PHD2 / SM-20 / HYPOXIA-INDUCIBLE FACTOR PROLYL HYDROXYLASE 2


Mass: 28096.941 Da / Num. of mol.: 3 / Fragment: CATALYTIC DOMAIN, RESIDUES 181-426
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9GZT9, procollagen-proline 4-dioxygenase, hypoxia-inducible factor-proline dioxygenase, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular ...References: UniProt: Q9GZT9, procollagen-proline 4-dioxygenase, hypoxia-inducible factor-proline dioxygenase, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-R8J / 6-(5-oxo-4-(1H-1,2,3-triazol-1-yl)-2,5-dihydro-1H-pyrazol-1-yl)nicotinic acid


Mass: 272.220 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H8N6O3

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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: 3.51 Å3/Da / Density % sol: 64.96 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6 M SODIUM CITRATE/CITRIC ACID PH 6.5, SITTING DROP, 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 7, 2012 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.3→44.73 Å / Num. obs: 17598 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 71.57 Å2 / Rmerge(I) obs: 0.22 / Net I/σ(I): 6.7
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BQY

4bqy


Resolution: 3.3→44.727 Å / SU ML: 0.39 / σ(F): 1.35 / Phase error: 22.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2266 894 5.1 %
Rwork0.2023 --
obs0.1916 17566 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.0108 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 63.5 Å2
Baniso -1Baniso -2Baniso -3
1-8.25 Å20 Å20 Å2
2--8.25 Å20 Å2
3----16.5 Å2
Refinement stepCycle: LAST / Resolution: 3.3→44.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4697 0 63 0 4760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074876
X-RAY DIFFRACTIONf_angle_d0.9756638
X-RAY DIFFRACTIONf_dihedral_angle_d15.0241724
X-RAY DIFFRACTIONf_chiral_restr0.032709
X-RAY DIFFRACTIONf_plane_restr0.004871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3001-3.50680.30831620.28132747X-RAY DIFFRACTION100
3.5068-3.77740.27081560.24472790X-RAY DIFFRACTION100
3.7774-4.15730.26841540.2052761X-RAY DIFFRACTION100
4.1573-4.75830.18611540.15892786X-RAY DIFFRACTION99
4.7583-5.99270.18541290.16672736X-RAY DIFFRACTION97
5.9927-44.73110.19011390.16432852X-RAY DIFFRACTION99
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)
10.01260.0018-0.00070.0140.0120.00920.0979-0.1075-0.22630.1790.09170.084-0.0810.0266-0.00040.41250.1067-0.02120.75930.02630.39913.922526.93098.9969
20.0353-0.0164-0.03170.01070.01090.02530.0496-0.0688-0.07270.0927-0.1563-0.1929-0.09150.22640.00010.21490.04610.01170.5110.00030.4037-6.182125.332512.0689
30.06350.0334-0.00220.0206-0.0120.020.07940.0760.2821-0.3629-0.0341-0.0908-0.26970.24670.00020.7216-0.06450.04730.81850.23530.6899-9.294340.2932-5.8325
40.0324-0.00450.01550.02970.04810.08030.12280.19380.01850.0320.119-0.0031-0.20370.1765-00.29580.05420.08890.61970.01390.4743-6.044325.4139-0.919
50.008-0.0160.0110.02150.00340.0423-0.00170.02660.0330.02230.08960.009-0.1324-0.09150.00010.3490.09780.00480.51640.08190.3879-20.28327.88753.5303
60.0656-0.0034-0.03980.0124-0.03990.1021-0.0679-0.33820.24560.03990.11680.0915-0.2195-0.04180.00010.40920.01630.04090.55140.04880.5975-17.984433.814414.1647
70.10940.0488-0.04410.0661-0.07040.05770.12950.157-0.0495-0.0269-0.00650.0117-0.09310.002700.28550.09920.03950.57050.03320.3875-15.985626.80454.5004
80.18940.2597-0.06890.4736-0.21670.1869-0.0699-0.04420.1882-0.06290.2569-0.11710.0653-0.05710.03070.34160.15410.04270.4635-0.06990.3147-29.668914.5172-22.6288
93.48090.17322.88664.54872.3043.4218-0.6799-0.36780.54551.14760.38961.78820.14710.1370.27281.1786-0.2389-0.18541.0504-0.09031.0781-41.68844.1552-34.8513
100.15290.01760.0060.00440.00010.00090.07020.3885-0.0713-0.05460.04210.0271-0.17320.08280.00930.76740.2550.07930.5770.23430.6285-41.945650.7647-0.6755
110.0084-0.0076-0.01140.02140.0140.0128-0.1135-0.10660.0382-0.1188-0.1963-0.0348-0.1167-0.08120.0011.33330.41520.01070.9728-0.08771.2728-46.400959.711322.2474
120.02020.0189-0.01140.0156-0.010.00610.0085-0.09120.0546-0.0152-0.19030.1909-0.1263-0.0770.00030.9680.44430.16111.02920.15211.045-55.227951.086422.6197
130.20880.08780.0630.0770.01150.0521-0.023-0.13220.03190.06430.10160.1799-0.4446-0.48170.01970.62180.41330.06210.60620.20270.6691-49.61645.268610.3623
140.0731-0.0423-0.02960.04-0.0390.14220.2468-0.0121-0.20550.16520.0043-0.0122-0.16280.26580.00030.54810.22470.04770.71990.0920.5118-34.109143.150213.7165
150.5326-0.1655-0.22290.16970.03810.1003-0.1451-0.20540.3213-0.01150.1907-0.00220.0249-0.09940.10980.54440.34710.03490.50580.24310.5117-41.776843.611412.4636
160.02940.01290.0080.0125-0.00430.0083-0.14780.0050.0408-0.0439-0.1425-0.05590.072-0.17410.00130.7170.4066-0.06881.04140.20660.8927-64.367433.21317.3076
170.0353-0.05360.05110.2062-0.09160.07860.12310.02460.2171-0.1013-0.00550.1323-0.0335-0.11470.13130.37110.2910.0730.78050.03280.4237-49.755517.6002-18.3532
180.13510.0429-0.14970.08230.01250.23440.2242-0.1362-0.3111-0.0593-0.04490.17480.4002-0.39080.02470.48290.0853-0.0230.55490.07930.4418-36.6454-0.0413-15.3972
190.04150.01790.0240.00940.0160.0310.40340.2018-0.2341-0.27220.1853-0.05-0.04850.03320.0010.35940.1073-0.03550.51010.02980.434-38.48958.4228-23.2344
200.02560.0295-0.01850.0421-0.02130.01220.2891-0.3280.0551-0.03950.013-0.0766-0.30550.07130.0010.32710.17150.02110.41940.0310.4109-35.78220.2647-18.8316
210.2104-0.0551-0.01080.01380.01490.0589-0.0268-0.23610.08660.22610.1179-0.01380.12070.08880.06650.03880.49320.24420.263-0.07780.1847-33.67929.0864-5.1653
220.0112-0.0097-0.00220.00730.00260.001-0.0633-0.07930.09180.2091-0.00720.25510.01370.0561-0.00010.87250.03670.06540.58630.22870.6647-45.3304-2.8181-2.9378
230.0812-0.0788-0.00240.1274-0.10750.1948-0.035-0.3143-0.0050.24380.2720.0298-0.0051-0.43580.00860.31220.11280.03230.51010.03340.3874-42.579411.248-2.6192
240.0487-0.0325-0.03160.02050.02140.0619-0.1405-0.092-0.03270.0864-0.06170.17430.04350.0371-0.0480.25910.25820.02580.31480.06830.3194-34.17248.8651-12.1013
250.00220.00490.00470.01380.00410.01710.22310.02520.0482-0.0060.36080.17320.0410.2204-0.00020.53760.06190.03640.63790.03990.5997-21.011224.9934-13.7118
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 184 THROUGH 197 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 198 THROUGH 214 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 215 THROUGH 266 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 267 THROUGH 303 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 304 THROUGH 329 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 330 THROUGH 353 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 354 THROUGH 402 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 403 THROUGH 418 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 419 THROUGH 419 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 188 THROUGH 215 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 216 THROUGH 232 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 233 THROUGH 266 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 267 THROUGH 329 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 330 THROUGH 352 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 353 THROUGH 392 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 393 THROUGH 404 )
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 188 THROUGH 204 )
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESID 205 THROUGH 266 )
19X-RAY DIFFRACTION19CHAIN 'C' AND (RESID 267 THROUGH 282 )
20X-RAY DIFFRACTION20CHAIN 'C' AND (RESID 283 THROUGH 297 )
21X-RAY DIFFRACTION21CHAIN 'C' AND (RESID 298 THROUGH 329 )
22X-RAY DIFFRACTION22CHAIN 'C' AND (RESID 330 THROUGH 342 )
23X-RAY DIFFRACTION23CHAIN 'C' AND (RESID 343 THROUGH 382 )
24X-RAY DIFFRACTION24CHAIN 'C' AND (RESID 383 THROUGH 392 )
25X-RAY DIFFRACTION25CHAIN 'C' AND (RESID 393 THROUGH 405 )

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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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