4Y30
Crystal structure of human protein arginine methyltransferase PRMT6 bound to SAH and EPZ020411
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003682 | molecular_function | chromatin binding |
| A | 0005515 | molecular_function | protein binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005654 | cellular_component | nucleoplasm |
| A | 0005730 | cellular_component | nucleolus |
| A | 0006284 | biological_process | base-excision repair |
| A | 0006338 | biological_process | chromatin remodeling |
| A | 0006355 | biological_process | regulation of DNA-templated transcription |
| A | 0008469 | molecular_function | obsolete histone arginine N-methyltransferase activity |
| A | 0010468 | biological_process | regulation of gene expression |
| A | 0010821 | biological_process | regulation of mitochondrion organization |
| A | 0016274 | molecular_function | protein-arginine N-methyltransferase activity |
| A | 0018216 | biological_process | peptidyl-arginine methylation |
| A | 0035241 | molecular_function | protein-arginine omega-N monomethyltransferase activity |
| A | 0035242 | molecular_function | protein-arginine omega-N asymmetric methyltransferase activity |
| A | 0042054 | molecular_function | histone methyltransferase activity |
| A | 0042393 | molecular_function | histone binding |
| A | 0044020 | molecular_function | histone H4R3 methyltransferase activity |
| A | 0045652 | biological_process | regulation of megakaryocyte differentiation |
| A | 0045892 | biological_process | negative regulation of DNA-templated transcription |
| A | 0070611 | molecular_function | histone H3R2 methyltransferase activity |
| A | 0070612 | molecular_function | histone H2AR3 methyltransferase activity |
| A | 0090068 | biological_process | positive regulation of cell cycle process |
| A | 0140938 | molecular_function | histone H3 methyltransferase activity |
| A | 2000059 | biological_process | negative regulation of ubiquitin-dependent protein catabolic process |
| B | 0003682 | molecular_function | chromatin binding |
| B | 0005515 | molecular_function | protein binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005654 | cellular_component | nucleoplasm |
| B | 0005730 | cellular_component | nucleolus |
| B | 0006284 | biological_process | base-excision repair |
| B | 0006338 | biological_process | chromatin remodeling |
| B | 0006355 | biological_process | regulation of DNA-templated transcription |
| B | 0008469 | molecular_function | obsolete histone arginine N-methyltransferase activity |
| B | 0010468 | biological_process | regulation of gene expression |
| B | 0010821 | biological_process | regulation of mitochondrion organization |
| B | 0016274 | molecular_function | protein-arginine N-methyltransferase activity |
| B | 0018216 | biological_process | peptidyl-arginine methylation |
| B | 0035241 | molecular_function | protein-arginine omega-N monomethyltransferase activity |
| B | 0035242 | molecular_function | protein-arginine omega-N asymmetric methyltransferase activity |
| B | 0042054 | molecular_function | histone methyltransferase activity |
| B | 0042393 | molecular_function | histone binding |
| B | 0044020 | molecular_function | histone H4R3 methyltransferase activity |
| B | 0045652 | biological_process | regulation of megakaryocyte differentiation |
| B | 0045892 | biological_process | negative regulation of DNA-templated transcription |
| B | 0070611 | molecular_function | histone H3R2 methyltransferase activity |
| B | 0070612 | molecular_function | histone H2AR3 methyltransferase activity |
| B | 0090068 | biological_process | positive regulation of cell cycle process |
| B | 0140938 | molecular_function | histone H3 methyltransferase activity |
| B | 2000059 | biological_process | negative regulation of ubiquitin-dependent protein catabolic process |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 24 |
| Details | binding site for residue SAH A 401 |
| Chain | Residue |
| A | TYR48 |
| A | GLU112 |
| A | ALA113 |
| A | SER114 |
| A | GLY138 |
| A | PRO139 |
| A | VAL140 |
| A | GLU141 |
| A | GLU155 |
| A | MET166 |
| A | SER169 |
| A | TYR51 |
| A | 49L402 |
| A | HOH594 |
| A | HOH604 |
| A | HOH610 |
| A | HOH611 |
| A | MET60 |
| A | ARG66 |
| A | GLY90 |
| A | ALA91 |
| A | GLY92 |
| A | ILE95 |
| A | LEU96 |
| site_id | AC2 |
| Number of Residues | 13 |
| Details | binding site for residue 49L A 402 |
| Chain | Residue |
| A | LEU46 |
| A | TYR51 |
| A | VAL56 |
| A | GLU59 |
| A | GLU155 |
| A | TRP156 |
| A | MET157 |
| A | TYR159 |
| A | HIS163 |
| A | GLU164 |
| A | HIS317 |
| A | SAH401 |
| A | HOH639 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | binding site for residue MG A 403 |
| Chain | Residue |
| A | HOH507 |
| A | HOH511 |
| A | HOH536 |
| A | HOH580 |
| A | HOH581 |
| A | HOH736 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | binding site for residue GOL A 404 |
| Chain | Residue |
| A | ALA115 |
| A | TRP117 |
| A | GLN118 |
| B | GLN251 |
| B | ARG276 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | binding site for residue GOL A 405 |
| Chain | Residue |
| A | ARG121 |
| A | HOH528 |
| B | ARG252 |
| B | PHE253 |
| B | ALA254 |
| site_id | AC6 |
| Number of Residues | 24 |
| Details | binding site for residue SAH B 401 |
| Chain | Residue |
| B | TYR47 |
| B | TYR51 |
| B | MET60 |
| B | ARG66 |
| B | GLY90 |
| B | ALA91 |
| B | ILE95 |
| B | LEU96 |
| B | GLU112 |
| B | ALA113 |
| B | SER114 |
| B | GLY138 |
| B | PRO139 |
| B | VAL140 |
| B | GLU141 |
| B | GLU155 |
| B | MET166 |
| B | SER169 |
| B | 49L402 |
| B | HOH566 |
| B | HOH576 |
| B | HOH578 |
| B | HOH580 |
| B | HOH681 |
| site_id | AC7 |
| Number of Residues | 14 |
| Details | binding site for residue 49L B 402 |
| Chain | Residue |
| B | ARG43 |
| B | LEU46 |
| B | TYR51 |
| B | VAL56 |
| B | GLU59 |
| B | GLU155 |
| B | TRP156 |
| B | MET157 |
| B | TYR159 |
| B | GLU164 |
| B | HIS317 |
| B | ASN349 |
| B | SAH401 |
| B | HOH675 |
| site_id | AC8 |
| Number of Residues | 10 |
| Details | binding site for residue GOL B 403 |
| Chain | Residue |
| B | HOH600 |
| B | HOH754 |
| B | LEU162 |
| B | SER165 |
| B | PRO345 |
| B | PRO350 |
| B | ARG351 |
| B | ARG352 |
| B | LEU353 |
| B | HOH588 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 660 |
| Details | Domain: {"description":"SAM-dependent MTase PRMT-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU01015","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | Active site: {"evidences":[{"evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 8 |
| Details | Binding site: {} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"32828318","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 10 |
| Details | Compositional bias: {"description":"Basic and acidic residues","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 3 |
| Details | Modified residue: {"description":"Asymmetric dimethylarginine; by autocatalysis","evidences":[{"source":"PubMed","id":"23866860","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
