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4Y30

Crystal structure of human protein arginine methyltransferase PRMT6 bound to SAH and EPZ020411

Functional Information from GO Data
ChainGOidnamespacecontents
A0000122biological_processnegative regulation of transcription by RNA polymerase II
A0003682molecular_functionchromatin binding
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005654cellular_componentnucleoplasm
A0005730cellular_componentnucleolus
A0006281biological_processDNA repair
A0006284biological_processbase-excision repair
A0006325biological_processchromatin organization
A0006338biological_processchromatin remodeling
A0006355biological_processregulation of DNA-templated transcription
A0006974biological_processDNA damage response
A0008168molecular_functionmethyltransferase activity
A0008469molecular_functionhistone arginine N-methyltransferase activity
A0010821biological_processregulation of mitochondrion organization
A0016274molecular_functionprotein-arginine N-methyltransferase activity
A0016740molecular_functiontransferase activity
A0018216biological_processpeptidyl-arginine methylation
A0032259biological_processmethylation
A0033554biological_processcellular response to stress
A0035241molecular_functionprotein-arginine omega-N monomethyltransferase activity
A0035242molecular_functionprotein-arginine omega-N asymmetric methyltransferase activity
A0042054molecular_functionhistone methyltransferase activity
A0042393molecular_functionhistone binding
A0044020molecular_functionhistone H4R3 methyltransferase activity
A0045652biological_processregulation of megakaryocyte differentiation
A0045892biological_processnegative regulation of DNA-templated transcription
A0070611molecular_functionhistone H3R2 methyltransferase activity
A0070612molecular_functionhistone H2AR3 methyltransferase activity
A0090398biological_processcellular senescence
A0140938molecular_functionhistone H3 methyltransferase activity
A1901796biological_processregulation of signal transduction by p53 class mediator
A2000059biological_processnegative regulation of ubiquitin-dependent protein catabolic process
B0000122biological_processnegative regulation of transcription by RNA polymerase II
B0003682molecular_functionchromatin binding
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005654cellular_componentnucleoplasm
B0005730cellular_componentnucleolus
B0006281biological_processDNA repair
B0006284biological_processbase-excision repair
B0006325biological_processchromatin organization
B0006338biological_processchromatin remodeling
B0006355biological_processregulation of DNA-templated transcription
B0006974biological_processDNA damage response
B0008168molecular_functionmethyltransferase activity
B0008469molecular_functionhistone arginine N-methyltransferase activity
B0010821biological_processregulation of mitochondrion organization
B0016274molecular_functionprotein-arginine N-methyltransferase activity
B0016740molecular_functiontransferase activity
B0018216biological_processpeptidyl-arginine methylation
B0032259biological_processmethylation
B0033554biological_processcellular response to stress
B0035241molecular_functionprotein-arginine omega-N monomethyltransferase activity
B0035242molecular_functionprotein-arginine omega-N asymmetric methyltransferase activity
B0042054molecular_functionhistone methyltransferase activity
B0042393molecular_functionhistone binding
B0044020molecular_functionhistone H4R3 methyltransferase activity
B0045652biological_processregulation of megakaryocyte differentiation
B0045892biological_processnegative regulation of DNA-templated transcription
B0070611molecular_functionhistone H3R2 methyltransferase activity
B0070612molecular_functionhistone H2AR3 methyltransferase activity
B0090398biological_processcellular senescence
B0140938molecular_functionhistone H3 methyltransferase activity
B1901796biological_processregulation of signal transduction by p53 class mediator
B2000059biological_processnegative regulation of ubiquitin-dependent protein catabolic process
Functional Information from PDB Data
site_idAC1
Number of Residues24
Detailsbinding site for residue SAH A 401
ChainResidue
ATYR48
AGLU112
AALA113
ASER114
AGLY138
APRO139
AVAL140
AGLU141
AGLU155
AMET166
ASER169
ATYR51
A49L402
AHOH594
AHOH604
AHOH610
AHOH611
AMET60
AARG66
AGLY90
AALA91
AGLY92
AILE95
ALEU96

site_idAC2
Number of Residues13
Detailsbinding site for residue 49L A 402
ChainResidue
ALEU46
ATYR51
AVAL56
AGLU59
AGLU155
ATRP156
AMET157
ATYR159
AHIS163
AGLU164
AHIS317
ASAH401
AHOH639

site_idAC3
Number of Residues6
Detailsbinding site for residue MG A 403
ChainResidue
AHOH507
AHOH511
AHOH536
AHOH580
AHOH581
AHOH736

site_idAC4
Number of Residues5
Detailsbinding site for residue GOL A 404
ChainResidue
AALA115
ATRP117
AGLN118
BGLN251
BARG276

site_idAC5
Number of Residues5
Detailsbinding site for residue GOL A 405
ChainResidue
AARG121
AHOH528
BARG252
BPHE253
BALA254

site_idAC6
Number of Residues24
Detailsbinding site for residue SAH B 401
ChainResidue
BTYR47
BTYR51
BMET60
BARG66
BGLY90
BALA91
BILE95
BLEU96
BGLU112
BALA113
BSER114
BGLY138
BPRO139
BVAL140
BGLU141
BGLU155
BMET166
BSER169
B49L402
BHOH566
BHOH576
BHOH578
BHOH580
BHOH681

site_idAC7
Number of Residues14
Detailsbinding site for residue 49L B 402
ChainResidue
BARG43
BLEU46
BTYR51
BVAL56
BGLU59
BGLU155
BTRP156
BMET157
BTYR159
BGLU164
BHIS317
BASN349
BSAH401
BHOH675

site_idAC8
Number of Residues10
Detailsbinding site for residue GOL B 403
ChainResidue
BHOH600
BHOH754
BLEU162
BSER165
BPRO345
BPRO350
BARG351
BARG352
BLEU353
BHOH588

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues660
DetailsDomain: {"description":"SAM-dependent MTase PRMT-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU01015","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues4
DetailsActive site: {"evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues2
DetailsBinding site: {"evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues8
DetailsBinding site: {}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues10
DetailsCompositional bias: {"description":"Basic and acidic residues","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues3
DetailsModified residue: {"description":"Asymmetric dimethylarginine; by autocatalysis","evidences":[{"source":"PubMed","id":"23866860","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

238895

PDB entries from 2025-07-16

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