5XXD
Crystal structure of SmyD3 in complex with covalent inhibitor 1
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000978 | molecular_function | RNA polymerase II cis-regulatory region sequence-specific DNA binding |
| A | 0000993 | molecular_function | RNA polymerase II complex binding |
| A | 0001162 | molecular_function | RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding |
| A | 0005515 | molecular_function | protein binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005654 | cellular_component | nucleoplasm |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0006325 | biological_process | chromatin organization |
| A | 0006334 | biological_process | nucleosome assembly |
| A | 0008168 | molecular_function | methyltransferase activity |
| A | 0008270 | molecular_function | zinc ion binding |
| A | 0014904 | biological_process | myotube cell development |
| A | 0016740 | molecular_function | transferase activity |
| A | 0032259 | biological_process | methylation |
| A | 0042054 | molecular_function | histone methyltransferase activity |
| A | 0045184 | biological_process | establishment of protein localization |
| A | 0045944 | biological_process | positive regulation of transcription by RNA polymerase II |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0071549 | biological_process | cellular response to dexamethasone stimulus |
| A | 0140939 | molecular_function | histone H4 methyltransferase activity |
| A | 0140954 | molecular_function | histone H3K36 dimethyltransferase activity |
| A | 0140999 | molecular_function | histone H3K4 trimethyltransferase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 22 |
| Details | binding site for residue SAM A 501 |
| Chain | Residue |
| A | ARG14 |
| A | LEU204 |
| A | ASN205 |
| A | HIS206 |
| A | TYR239 |
| A | TYR257 |
| A | PHE259 |
| A | 8NR505 |
| A | HOH604 |
| A | HOH614 |
| A | HOH694 |
| A | ASN16 |
| A | HOH704 |
| A | HOH713 |
| A | HOH714 |
| A | TYR124 |
| A | GLU130 |
| A | ASN132 |
| A | CYS180 |
| A | ASN181 |
| A | SER202 |
| A | LEU203 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | binding site for residue ZN A 502 |
| Chain | Residue |
| A | CYS208 |
| A | CYS261 |
| A | CYS263 |
| A | CYS266 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | binding site for residue ZN A 503 |
| Chain | Residue |
| A | CYS62 |
| A | CYS65 |
| A | HIS83 |
| A | CYS87 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | binding site for residue ZN A 504 |
| Chain | Residue |
| A | CYS49 |
| A | CYS52 |
| A | CYS71 |
| A | CYS75 |
| site_id | AC5 |
| Number of Residues | 16 |
| Details | binding site for residue 8NR A 505 |
| Chain | Residue |
| A | CYS180 |
| A | ASN181 |
| A | SER182 |
| A | PHE183 |
| A | THR184 |
| A | CYS186 |
| A | MET190 |
| A | ILE214 |
| A | PHE216 |
| A | ILE237 |
| A | CYS238 |
| A | TYR239 |
| A | TYR257 |
| A | VAL368 |
| A | SAM501 |
| A | HOH630 |
Functional Information from PROSITE/UniProt
| site_id | PS01360 |
| Number of Residues | 39 |
| Details | ZF_MYND_1 Zinc finger MYND-type signature. Cdr..Cllgkeklmr........CsqCrvakYCsakCqkkawpd..Hkre.C |
| Chain | Residue | Details |
| A | CYS49-CYS87 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 236 |
| Details | Domain: {"description":"SET","evidences":[{"source":"PROSITE-ProRule","id":"PRU00190","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 38 |
| Details | Zinc finger: {"description":"MYND-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00134","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 3 |
| Details | Binding site: {"evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"APR-2010","submissionDatabase":"PDB data bank","title":"Crystal structure of human histone-lysine n-methyltransferase SMYD3 in complex with S-adenosyl-L-methionine.","authoringGroup":["Structural genomics consortium (SGC)"]}}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00134","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 5 |
| Details | Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00190","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"APR-2010","submissionDatabase":"PDB data bank","title":"Crystal structure of human histone-lysine n-methyltransferase SMYD3 in complex with S-adenosyl-L-methionine.","authoringGroup":["Structural genomics consortium (SGC)"]}}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 1 |
| Details | Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
