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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

6HGT

Crystal structure of human KDM4A complexed with co-substrate analog NOG and histone H3 peptide with K9R mutation

Functional Information from PDB Data
site_idAC1
Number of Residues4
Detailsbinding site for residue ZN A 401
ChainResidue
AHIS188
AGLU190
AHIS276
AOGA403
site_idAC2
Number of Residues4
Detailsbinding site for residue ZN A 402
ChainResidue
ACYS234
AHIS240
ACYS306
ACYS308
site_idAC3
Number of Residues11
Detailsbinding site for residue OGA A 403
ChainResidue
APHE185
AHIS188
AGLU190
ASER196
AASN198
ALYS206
AHIS276
ASER288
AZN401
AHOH505
ATYR132
site_idAC4
Number of Residues5
Detailsbinding site for residue ZN B 401
ChainResidue
BHIS188
BGLU190
BHIS276
BOGA403
BHOH582
site_idAC5
Number of Residues4
Detailsbinding site for residue ZN B 402
ChainResidue
BCYS234
BHIS240
BCYS306
BCYS308
site_idAC6
Number of Residues11
Detailsbinding site for residue OGA B 403
ChainResidue
BTYR132
BPHE185
BHIS188
BGLU190
BSER196
BASN198
BLYS206
BHIS276
BSER288
BZN401
BHOH521
site_idAC7
Number of Residues5
Detailsbinding site for residue ZN C 401
ChainResidue
CHIS188
CGLU190
CHIS276
COGA403
CHOH530
site_idAC8
Number of Residues4
Detailsbinding site for residue ZN C 402
ChainResidue
CCYS234
CHIS240
CCYS306
CCYS308
site_idAC9
Number of Residues12
Detailsbinding site for residue OGA C 403
ChainResidue
CTYR132
CPHE185
CHIS188
CGLU190
CSER196
CASN198
CLYS206
CHIS276
CSER288
CZN401
GARG9
GHOH102
site_idAD1
Number of Residues4
Detailsbinding site for residue ZN D 401
ChainResidue
DHIS188
DGLU190
DHIS276
DOGA403
site_idAD2
Number of Residues4
Detailsbinding site for residue ZN D 402
ChainResidue
DCYS234
DHIS240
DCYS306
DCYS308
site_idAD3
Number of Residues12
Detailsbinding site for residue OGA D 403
ChainResidue
DTYR132
DPHE185
DHIS188
DGLU190
DSER196
DASN198
DLYS206
DHIS276
DSER288
DZN401
DHOH504
HARG9
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues168
DetailsDomain: {"description":"JmjN","evidences":[{"source":"PROSITE-ProRule","id":"PRU00537","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues664
DetailsDomain: {"description":"JmjC","evidences":[{"source":"PROSITE-ProRule","id":"PRU00538","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues12
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"16677698","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues8
DetailsBinding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00538","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"16677698","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26741168","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"16677698","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26741168","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues16
DetailsBinding site: {"evidences":[{"source":"PDB","id":"5F2W","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F32","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F37","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F39","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F3E","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F3G","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F5I","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"UniProtKB","id":"B2RXH2","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues4
DetailsModified residue: {"description":"Symmetric dimethylarginine; by PRMT5; alternate","evidences":[{"source":"UniProtKB","id":"P84244","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues4
DetailsModified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"PubMed","id":"11242053","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16185088","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16267050","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16457588","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17194708","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"7309716","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues4
DetailsModified residue: {"description":"Phosphoserine; alternate; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5","evidences":[{"source":"PubMed","id":"10464286","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11856369","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12560483","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15681610","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15851689","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16185088","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues4
DetailsModified residue: {"description":"Phosphothreonine; by PKC","evidences":[{"source":"PubMed","id":"12560483","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18066052","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22901803","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
Catalytic Information from CSA
site_idMCSA1
Number of Residues6
DetailsM-CSA 370
ChainResidueDetails
AGLY170hydrogen bond acceptor, steric role
ATYR177hydrogen bond donor, steric role
AHIS188metal ligand
AGLU190attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role
AHIS276metal ligand
ASER288hydrogen bond donor, steric role
site_idMCSA2
Number of Residues6
DetailsM-CSA 370
ChainResidueDetails
BGLY170hydrogen bond acceptor, steric role
BTYR177hydrogen bond donor, steric role
BHIS188metal ligand
BGLU190attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role
BHIS276metal ligand
BSER288hydrogen bond donor, steric role
site_idMCSA3
Number of Residues6
DetailsM-CSA 370
ChainResidueDetails
CGLY170hydrogen bond acceptor, steric role
CTYR177hydrogen bond donor, steric role
CHIS188metal ligand
CGLU190attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role
CHIS276metal ligand
CSER288hydrogen bond donor, steric role
site_idMCSA4
Number of Residues6
DetailsM-CSA 370
ChainResidueDetails
DGLY170hydrogen bond acceptor, steric role
DTYR177hydrogen bond donor, steric role
DHIS188metal ligand
DGLU190attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role
DHIS276metal ligand
DSER288hydrogen bond donor, steric role

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PDB entries from 2026-04-01

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