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6P7I

Crystal structure of Human PRMT6 in complex with S-Adenosyl-L-Homocysteine and YS17-117 Compound

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
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
A0035241molecular_functionprotein-arginine omega-N monomethyltransferase activity
A0035242molecular_functionprotein-arginine omega-N asymmetric methyltransferase activity
A0036211biological_processprotein modification process
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
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
B0035241molecular_functionprotein-arginine omega-N monomethyltransferase activity
B0035242molecular_functionprotein-arginine omega-N asymmetric methyltransferase activity
B0036211biological_processprotein modification process
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
C0000122biological_processnegative regulation of transcription by RNA polymerase II
C0003682molecular_functionchromatin binding
C0005515molecular_functionprotein binding
C0005634cellular_componentnucleus
C0005654cellular_componentnucleoplasm
C0005730cellular_componentnucleolus
C0006281biological_processDNA repair
C0006284biological_processbase-excision repair
C0006325biological_processchromatin organization
C0006338biological_processchromatin remodeling
C0006974biological_processDNA damage response
C0008168molecular_functionmethyltransferase activity
C0008469molecular_functionhistone arginine N-methyltransferase activity
C0010821biological_processregulation of mitochondrion organization
C0016274molecular_functionprotein-arginine N-methyltransferase activity
C0016740molecular_functiontransferase activity
C0018216biological_processpeptidyl-arginine methylation
C0032259biological_processmethylation
C0035241molecular_functionprotein-arginine omega-N monomethyltransferase activity
C0035242molecular_functionprotein-arginine omega-N asymmetric methyltransferase activity
C0036211biological_processprotein modification process
C0042054molecular_functionhistone methyltransferase activity
C0042393molecular_functionhistone binding
C0044020molecular_functionhistone H4R3 methyltransferase activity
C0045652biological_processregulation of megakaryocyte differentiation
C0045892biological_processnegative regulation of DNA-templated transcription
C0070611molecular_functionhistone H3R2 methyltransferase activity
C0070612molecular_functionhistone H2AR3 methyltransferase activity
C0090398biological_processcellular senescence
C0140938molecular_functionhistone H3 methyltransferase activity
C1901796biological_processregulation of signal transduction by p53 class mediator
C2000059biological_processnegative regulation of ubiquitin-dependent protein catabolic process
D0000122biological_processnegative regulation of transcription by RNA polymerase II
D0003682molecular_functionchromatin binding
D0005515molecular_functionprotein binding
D0005634cellular_componentnucleus
D0005654cellular_componentnucleoplasm
D0005730cellular_componentnucleolus
D0006281biological_processDNA repair
D0006284biological_processbase-excision repair
D0006325biological_processchromatin organization
D0006338biological_processchromatin remodeling
D0006974biological_processDNA damage response
D0008168molecular_functionmethyltransferase activity
D0008469molecular_functionhistone arginine N-methyltransferase activity
D0010821biological_processregulation of mitochondrion organization
D0016274molecular_functionprotein-arginine N-methyltransferase activity
D0016740molecular_functiontransferase activity
D0018216biological_processpeptidyl-arginine methylation
D0032259biological_processmethylation
D0035241molecular_functionprotein-arginine omega-N monomethyltransferase activity
D0035242molecular_functionprotein-arginine omega-N asymmetric methyltransferase activity
D0036211biological_processprotein modification process
D0042054molecular_functionhistone methyltransferase activity
D0042393molecular_functionhistone binding
D0044020molecular_functionhistone H4R3 methyltransferase activity
D0045652biological_processregulation of megakaryocyte differentiation
D0045892biological_processnegative regulation of DNA-templated transcription
D0070611molecular_functionhistone H3R2 methyltransferase activity
D0070612molecular_functionhistone H2AR3 methyltransferase activity
D0090398biological_processcellular senescence
D0140938molecular_functionhistone H3 methyltransferase activity
D1901796biological_processregulation of signal transduction by p53 class mediator
D2000059biological_processnegative regulation of ubiquitin-dependent protein catabolic process
Functional Information from PDB Data
site_idAC1
Number of Residues21
Detailsbinding site for residue SAH A 401
ChainResidue
ATYR48
ASER114
APRO139
AVAL140
AGLU141
AGLU155
AMET166
ASER169
AO3P402
AHOH515
AHOH542
ATYR51
AHOH580
AHOH585
AMET60
AARG66
AGLY90
AALA91
ALEU96
AGLU112
AALA113

site_idAC2
Number of Residues12
Detailsbinding site for residue O3P A 402
ChainResidue
ATYR47
ACYS50
ATYR51
AVAL56
AGLU59
AGLU155
AMET157
ATYR159
AGLU164
AHIS317
ASAH401
AHOH616

site_idAC3
Number of Residues9
Detailsbinding site for residue GOL A 403
ChainResidue
ASER242
AGLY243
APRO311
AHOH622
BGLY243
BVAL246
BTYR280
BPHE312
BHOH549

site_idAC4
Number of Residues22
Detailsbinding site for residue SAH B 401
ChainResidue
BTYR47
BTYR48
BTYR51
BMET60
BARG66
BGLY90
BALA91
BLEU96
BGLU112
BALA113
BSER114
BPRO139
BVAL140
BGLU141
BGLU155
BMET166
BSER169
BO3P402
BHOH552
BHOH579
BHOH612
BHOH613

site_idAC5
Number of Residues12
Detailsbinding site for residue O3P B 402
ChainResidue
BTYR47
BCYS50
BTYR51
BVAL56
BGLU59
BGLU155
BMET157
BTYR159
BGLU164
BHIS317
BSAH401
BHOH606

site_idAC6
Number of Residues6
Detailsbinding site for residue GOL B 403
ChainResidue
BALA254
BGLN255
BVAL271
BGLY272
BHOH521
BHOH594

site_idAC7
Number of Residues23
Detailsbinding site for residue SAH C 401
ChainResidue
CO3P402
CHOH514
CHOH542
CHOH565
CHOH606
CHOH618
CTYR48
CTYR51
CMET60
CARG66
CGLY90
CALA91
CILE95
CLEU96
CGLU112
CALA113
CSER114
CPRO139
CVAL140
CGLU141
CGLU155
CMET166
CSER169

site_idAC8
Number of Residues13
Detailsbinding site for residue O3P C 402
ChainResidue
CTYR47
CCYS50
CTYR51
CVAL56
CGLU59
CGLU155
CMET157
CTYR159
CGLU164
CHIS317
CTRP318
CSAH401
CHOH638

site_idAC9
Number of Residues23
Detailsbinding site for residue SAH D 401
ChainResidue
DTYR48
DTYR51
DMET60
DARG66
DGLY90
DALA91
DILE95
DLEU96
DGLU112
DALA113
DSER114
DGLY138
DPRO139
DVAL140
DGLU141
DGLU155
DMET166
DSER169
DO3S402
DHOH526
DHOH602
DHOH604
DHOH605

site_idAD1
Number of Residues15
Detailsbinding site for Di-peptide O3S D 402 and CYS D 50
ChainResidue
DLEU46
DTYR47
DTYR48
DGLU49
DTYR51
DSER52
DASP53
DGLU59
DGLU155
DMET157
DTYR159
DGLU164
DHIS317
DSAH401
DHOH641

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues8
DetailsACT_SITE: ACT_SITE => ECO:0000250
ChainResidueDetails
AGLU155
AGLU164
BGLU155
BGLU164
CGLU155
CGLU164
DGLU155
DGLU164

site_idSWS_FT_FI2
Number of Residues4
DetailsBINDING: BINDING => ECO:0000250
ChainResidueDetails
AHIS57
BHIS57
CHIS57
DHIS57

site_idSWS_FT_FI3
Number of Residues16
DetailsBINDING:
ChainResidueDetails
AARG66
CGLY90
CGLU112
CGLU141
DARG66
DGLY90
DGLU112
DGLU141
AGLY90
AGLU112
AGLU141
BARG66
BGLY90
BGLU112
BGLU141
CARG66

site_idSWS_FT_FI4
Number of Residues4
DetailsMOD_RES: Phosphothreonine => ECO:0007744|PubMed:18691976, ECO:0007744|PubMed:23186163
ChainResidueDetails
ATHR21
BTHR21
CTHR21
DTHR21

site_idSWS_FT_FI5
Number of Residues12
DetailsMOD_RES: Asymmetric dimethylarginine; by autocatalysis => ECO:0000269|PubMed:23866860
ChainResidueDetails
AARG29
DARG29
DARG35
DARG37
AARG35
AARG37
BARG29
BARG35
BARG37
CARG29
CARG35
CARG37

218853

PDB entries from 2024-04-24

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