5PJO

PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 73)

> Summary

Summary for 5PJO

Group depositionPanDDA analysis group deposition of models of ground state datasets (G_1002021)
DescriptorLysine-specific demethylase 4D, ZINC ION, NICKEL (II) ION, ... (8 entities in total)
Functional Keywordspandda, sgc - diamond i04-1 fragment screening, jmj domain, epigenetics, oxidoreductase
Biological sourceHomo sapiens (Human)
Cellular locationNucleus  Q6B0I6
Total number of polymer chains1
Total molecular weight43130.77
Authors
Primary citation
Pearce, N.M.,Krojer, T.,Bradley, A.R.,Collins, P.,Nowak, R.P.,Talon, R.,Marsden, B.D.,Kelm, S.,Shi, J.,Deane, C.M.,von Delft, F.
A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.
Nat Commun, 8:15123-15123, 2017
PubMed: 28436492 (PDB entries with the same primary citation)
DOI: 10.1038/ncomms15123
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.35 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.18570.3%1.8%5.4%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5pjo
no rotation
Molmil generated image of 5pjo
rotated about x axis by 90°
Molmil generated image of 5pjo
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
ALysine-specific demethylase 4Dpolymer36442050.51
UniProt (Q6B0I6)
Pfam (PF02373)
Pfam (PF02375)
Homo sapiens (Human)JmjC domain-containing histone demethylation protein 3D,Jumonji domain-containing protein 2D
ZINC IONnon-polymer65.41
NICKEL (II) IONnon-polymer58.71
MAGNESIUM IONnon-polymer24.31
N-OXALYLGLYCINEnon-polymer147.11
1,2-ETHANEDIOLnon-polymer62.18
SULFATE IONnon-polymer96.13
waterwater18.0441

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight42050.5
Non-Polymers*Number of molecules15
Total molecular weight1080.2
All*Total molecular weight43130.8
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.35 Å)

Cell axes71.43771.437150.340
Cell angles90.0090.0090.00
SpacegroupP 43 21 2
Resolution limits29.40 - 1.35
the highest resolution shell value1.382 - 1.347
R-factor0.1583
R-work0.15730
the highest resolution shell value0.254
R-free0.17850
the highest resolution shell value0.261
RMSD bond length0.027
RMSD bond angle2.464

Data Collection Statistics

Resolution limits29.40 - 1.35
the highest resolution shell value -
Number of reflections86429
Rmerge_l_obs0.049
the highest resolution shell value0.710
Completeness99.7
Redundancy11.8
the highest resolution shell value5.3

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, SITTING DROP7298

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0072562cellular_componentblood microparticle
A0005654cellular_componentnucleoplasm
A0035861cellular_componentsite of double-strand break
A0051213molecular_functiondioxygenase activity
A0032452molecular_functionhistone demethylase activity
A0032454molecular_functionhistone demethylase activity (H3-K9 specific)
A0046872molecular_functionmetal ion binding
A0071479biological_processcellular response to ionizing radiation
A0000724biological_processdouble-strand break repair via homologous recombination
A0033169biological_processhistone H3-K9 demethylation
A0035563biological_processpositive regulation of chromatin binding
A2001034biological_processpositive regulation of double-strand break repair via nonhomologous end joining
A0001932biological_processregulation of protein phosphorylation
A0006355biological_processregulation of transcription, DNA-templated
A0006351biological_processtranscription, DNA-templated
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC14binding site for residue ZN A 401
ChainResidue
ACYS238
AHIS244
ACYS310
ACYS312

AC25binding site for residue NI A 402
ChainResidue
AHIS192
AGLU194
AHIS280
AOGA404
AHOH590

AC36binding site for residue MG A 403
ChainResidue
AASN65
AILE66
ASER67
AGLU68
AILE69
AVAL171

AC413binding site for residue OGA A 404
ChainResidue
ATYR136
APHE189
AHIS192
AGLU194
ASER200
AASN202
ALYS210
AHIS280
AALA292
ANI402
AEDO412
AHOH590
AHOH622

AC57binding site for residue EDO A 405
ChainResidue
ALYS150
AGLN151
ATRP152
AASN153
AHIS156
AHOH611
AHOH736

AC64binding site for residue EDO A 406
ChainResidue
APRO251
ATHR252
AARG263
AHOH532

AC78binding site for residue EDO A 407
ChainResidue
AGLU224
AALA240
APHE241
ALEU242
ATYR279
ASER308
AHOH510
AHOH519

AC87binding site for residue EDO A 408
ChainResidue
AASP64
AASN65
AILE66
ASER67
AGLU68
AARG82
AHOH574

AC94binding site for residue EDO A 409
ChainResidue
APHE118
AILE264
ATHR265
AHOH552

AD110binding site for residue EDO A 410
ChainResidue
ATRP57
ALYS58
AALA59
AARG60
ATYR63
ATYR203
AHOH502
AHOH520
AHOH571
AHOH685

AD26binding site for residue EDO A 411
ChainResidue
ASER80
ATHR87
ACYS168
ALYS305
AHOH525
AHOH536

AD36binding site for residue EDO A 412
ChainResidue
ATYR181
ASER200
AALA292
AASN294
AOGA404
AHOH590

AD46binding site for residue SO4 A 413
ChainResidue
AARG102
AHIS103
AASN106
AHOH507
AHOH648
AHOH703

AD58binding site for residue SO4 A 414
ChainResidue
AARG60
AGLU61
ATHR62
AASN65
AHOH504
AHOH554
AHOH591
AHOH747

AD64binding site for residue SO4 A 415
ChainResidue
AARG123
ALYS124
ALYS127
AASN128

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
EDO_5pjo_A_40591,2-ETHANEDIOL binding site
ChainResidueligand
AASN29EDO: 1,2-ETHANEDIOL
APHE31EDO: 1,2-ETHANEDIOL
ATHR149-ASN153EDO: 1,2-ETHANEDIOL
AHIS156-LEU157EDO: 1,2-ETHANEDIOL

EDO_5pjo_A_41071,2-ETHANEDIOL binding site
ChainResidueligand
ATRP57-ARG60EDO: 1,2-ETHANEDIOL
ATYR63EDO: 1,2-ETHANEDIOL
ATYR203EDO: 1,2-ETHANEDIOL
AGLY269EDO: 1,2-ETHANEDIOL

EDO_5pjo_A_40851,2-ETHANEDIOL binding site
ChainResidueligand
AASP64-GLU68EDO: 1,2-ETHANEDIOL

EDO_5pjo_A_41171,2-ETHANEDIOL binding site
ChainResidueligand
ASER80-GLY81EDO: 1,2-ETHANEDIOL
AVAL85-THR87EDO: 1,2-ETHANEDIOL
ALEU230-PHE231EDO: 1,2-ETHANEDIOL

EDO_5pjo_A_40971,2-ETHANEDIOL binding site
ChainResidueligand
APHE118-GLU119EDO: 1,2-ETHANEDIOL
AGLU122EDO: 1,2-ETHANEDIOL
ATHR211EDO: 1,2-ETHANEDIOL
AARG263-THR265EDO: 1,2-ETHANEDIOL

EDO_5pjo_A_40661,2-ETHANEDIOL binding site
ChainResidueligand
AGLU122EDO: 1,2-ETHANEDIOL
APRO251-THR252EDO: 1,2-ETHANEDIOL
ALYS255EDO: 1,2-ETHANEDIOL
APHE261EDO: 1,2-ETHANEDIOL
AARG263EDO: 1,2-ETHANEDIOL

OGA_5pjo_A_40414N-OXALYLGLYCINE binding site
ChainResidueligand
ATYR136OGA: N-OXALYLGLYCINE
ATYR181OGA: N-OXALYLGLYCINE
APHE189OGA: N-OXALYLGLYCINE
AHIS192OGA: N-OXALYLGLYCINE
AGLU194OGA: N-OXALYLGLYCINE
ASER200-ASN202OGA: N-OXALYLGLYCINE
ALYS210OGA: N-OXALYLGLYCINE
ATRP212OGA: N-OXALYLGLYCINE
ATHR274OGA: N-OXALYLGLYCINE
AHIS280OGA: N-OXALYLGLYCINE
AALA290OGA: N-OXALYLGLYCINE
AALA292OGA: N-OXALYLGLYCINE

EDO_5pjo_A_41271,2-ETHANEDIOL binding site
ChainResidueligand
ATYR179EDO: 1,2-ETHANEDIOL
ATYR181EDO: 1,2-ETHANEDIOL
AGLU194EDO: 1,2-ETHANEDIOL
ASER200EDO: 1,2-ETHANEDIOL
AALA292-ASN294EDO: 1,2-ETHANEDIOL

EDO_5pjo_A_40791,2-ETHANEDIOL binding site
ChainResidueligand
AGLU224EDO: 1,2-ETHANEDIOL
AARG228EDO: 1,2-ETHANEDIOL
AGLY239-ARG243EDO: 1,2-ETHANEDIOL
ATYR279EDO: 1,2-ETHANEDIOL
ASER308EDO: 1,2-ETHANEDIOL

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI11Zinc; via tele nitrogen. {ECO:0000244|PDB:5F5A, ECO:0000244|PDB:5F5C}
ChainResidueDetails
AHIS266

SWS_FT_FI23Iron; catalytic. {ECO:0000255|PROSITE- ProRule:PRU00538, ECO:0000305|PubMed:26741168}
ChainResidueDetails
AHIS214
AGLU216
AHIS302

SWS_FT_FI33Zinc. {ECO:0000244|PDB:5F5A, ECO:0000244|PDB:5F5C}
ChainResidueDetails
ACYS260
ACYS332
ACYS334

SWS_FT_FI442-oxoglutarate. {ECO:0000250|UniProtKB:B2RXH2}.
ChainResidueDetails
ATYR158
AASN224
ALYS232
ALYS267

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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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