6CSW
Crystal Structure of the Human vaccinia-related kinase bound to a N-methyl-N-propyl-dihydropteridine inhibitor
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000785 | cellular_component | chromatin |
| A | 0004672 | molecular_function | protein kinase activity |
| A | 0004674 | molecular_function | protein serine/threonine kinase activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005524 | molecular_function | ATP binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005654 | cellular_component | nucleoplasm |
| A | 0005730 | cellular_component | nucleolus |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005795 | cellular_component | Golgi stack |
| A | 0005829 | cellular_component | cytosol |
| A | 0006338 | biological_process | chromatin remodeling |
| A | 0006468 | biological_process | protein phosphorylation |
| A | 0006974 | biological_process | DNA damage response |
| A | 0007077 | biological_process | mitotic nuclear membrane disassembly |
| A | 0007165 | biological_process | signal transduction |
| A | 0015030 | cellular_component | Cajal body |
| A | 0016301 | molecular_function | kinase activity |
| A | 0016310 | biological_process | phosphorylation |
| A | 0019901 | molecular_function | protein kinase binding |
| A | 0030576 | biological_process | Cajal body organization |
| A | 0031175 | biological_process | neuron projection development |
| A | 0031492 | molecular_function | nucleosomal DNA binding |
| A | 0035175 | molecular_function | histone H3S10 kinase activity |
| A | 0042393 | molecular_function | histone binding |
| A | 0044024 | molecular_function | histone H2AS1 kinase activity |
| A | 0046777 | biological_process | protein autophosphorylation |
| A | 0051301 | biological_process | cell division |
| A | 0072354 | molecular_function | histone H3T3 kinase activity |
| A | 0090166 | biological_process | Golgi disassembly |
| A | 0106310 | molecular_function | protein serine kinase activity |
| A | 0120187 | biological_process | positive regulation of protein localization to chromatin |
| A | 0141003 | molecular_function | histone H2AX kinase activity |
| A | 2001222 | biological_process | regulation of neuron migration |
| B | 0000785 | cellular_component | chromatin |
| B | 0004672 | molecular_function | protein kinase activity |
| B | 0004674 | molecular_function | protein serine/threonine kinase activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005524 | molecular_function | ATP binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005654 | cellular_component | nucleoplasm |
| B | 0005730 | cellular_component | nucleolus |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005795 | cellular_component | Golgi stack |
| B | 0005829 | cellular_component | cytosol |
| B | 0006338 | biological_process | chromatin remodeling |
| B | 0006468 | biological_process | protein phosphorylation |
| B | 0006974 | biological_process | DNA damage response |
| B | 0007077 | biological_process | mitotic nuclear membrane disassembly |
| B | 0007165 | biological_process | signal transduction |
| B | 0015030 | cellular_component | Cajal body |
| B | 0016301 | molecular_function | kinase activity |
| B | 0016310 | biological_process | phosphorylation |
| B | 0019901 | molecular_function | protein kinase binding |
| B | 0030576 | biological_process | Cajal body organization |
| B | 0031175 | biological_process | neuron projection development |
| B | 0031492 | molecular_function | nucleosomal DNA binding |
| B | 0035175 | molecular_function | histone H3S10 kinase activity |
| B | 0042393 | molecular_function | histone binding |
| B | 0044024 | molecular_function | histone H2AS1 kinase activity |
| B | 0046777 | biological_process | protein autophosphorylation |
| B | 0051301 | biological_process | cell division |
| B | 0072354 | molecular_function | histone H3T3 kinase activity |
| B | 0090166 | biological_process | Golgi disassembly |
| B | 0106310 | molecular_function | protein serine kinase activity |
| B | 0120187 | biological_process | positive regulation of protein localization to chromatin |
| B | 0141003 | molecular_function | histone H2AX kinase activity |
| B | 2001222 | biological_process | regulation of neuron migration |
| C | 0000785 | cellular_component | chromatin |
| C | 0004672 | molecular_function | protein kinase activity |
| C | 0004674 | molecular_function | protein serine/threonine kinase activity |
| C | 0005515 | molecular_function | protein binding |
| C | 0005524 | molecular_function | ATP binding |
| C | 0005634 | cellular_component | nucleus |
| C | 0005654 | cellular_component | nucleoplasm |
| C | 0005730 | cellular_component | nucleolus |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005795 | cellular_component | Golgi stack |
| C | 0005829 | cellular_component | cytosol |
| C | 0006338 | biological_process | chromatin remodeling |
| C | 0006468 | biological_process | protein phosphorylation |
| C | 0006974 | biological_process | DNA damage response |
| C | 0007077 | biological_process | mitotic nuclear membrane disassembly |
| C | 0007165 | biological_process | signal transduction |
| C | 0015030 | cellular_component | Cajal body |
| C | 0016301 | molecular_function | kinase activity |
| C | 0016310 | biological_process | phosphorylation |
| C | 0019901 | molecular_function | protein kinase binding |
| C | 0030576 | biological_process | Cajal body organization |
| C | 0031175 | biological_process | neuron projection development |
| C | 0031492 | molecular_function | nucleosomal DNA binding |
| C | 0035175 | molecular_function | histone H3S10 kinase activity |
| C | 0042393 | molecular_function | histone binding |
| C | 0044024 | molecular_function | histone H2AS1 kinase activity |
| C | 0046777 | biological_process | protein autophosphorylation |
| C | 0051301 | biological_process | cell division |
| C | 0072354 | molecular_function | histone H3T3 kinase activity |
| C | 0090166 | biological_process | Golgi disassembly |
| C | 0106310 | molecular_function | protein serine kinase activity |
| C | 0120187 | biological_process | positive regulation of protein localization to chromatin |
| C | 0141003 | molecular_function | histone H2AX kinase activity |
| C | 2001222 | biological_process | regulation of neuron migration |
| D | 0000785 | cellular_component | chromatin |
| D | 0004672 | molecular_function | protein kinase activity |
| D | 0004674 | molecular_function | protein serine/threonine kinase activity |
| D | 0005515 | molecular_function | protein binding |
| D | 0005524 | molecular_function | ATP binding |
| D | 0005634 | cellular_component | nucleus |
| D | 0005654 | cellular_component | nucleoplasm |
| D | 0005730 | cellular_component | nucleolus |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0005795 | cellular_component | Golgi stack |
| D | 0005829 | cellular_component | cytosol |
| D | 0006338 | biological_process | chromatin remodeling |
| D | 0006468 | biological_process | protein phosphorylation |
| D | 0006974 | biological_process | DNA damage response |
| D | 0007077 | biological_process | mitotic nuclear membrane disassembly |
| D | 0007165 | biological_process | signal transduction |
| D | 0015030 | cellular_component | Cajal body |
| D | 0016301 | molecular_function | kinase activity |
| D | 0016310 | biological_process | phosphorylation |
| D | 0019901 | molecular_function | protein kinase binding |
| D | 0030576 | biological_process | Cajal body organization |
| D | 0031175 | biological_process | neuron projection development |
| D | 0031492 | molecular_function | nucleosomal DNA binding |
| D | 0035175 | molecular_function | histone H3S10 kinase activity |
| D | 0042393 | molecular_function | histone binding |
| D | 0044024 | molecular_function | histone H2AS1 kinase activity |
| D | 0046777 | biological_process | protein autophosphorylation |
| D | 0051301 | biological_process | cell division |
| D | 0072354 | molecular_function | histone H3T3 kinase activity |
| D | 0090166 | biological_process | Golgi disassembly |
| D | 0106310 | molecular_function | protein serine kinase activity |
| D | 0120187 | biological_process | positive regulation of protein localization to chromatin |
| D | 0141003 | molecular_function | histone H2AX kinase activity |
| D | 2001222 | biological_process | regulation of neuron migration |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 A 401 |
| Chain | Residue |
| A | GLN95 |
| A | HIS171 |
| A | HOH505 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 A 402 |
| Chain | Residue |
| A | GLU280 |
| A | HOH554 |
| B | LYS314 |
| B | HOH534 |
| C | SO4403 |
| site_id | AC3 |
| Number of Residues | 3 |
| Details | binding site for residue ACT A 403 |
| Chain | Residue |
| A | HIS258 |
| A | HOH546 |
| A | ARG148 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | binding site for residue PG4 A 404 |
| Chain | Residue |
| A | THR30 |
| A | LEU118 |
| A | HIS119 |
| A | ASP120 |
| D | LYS301 |
| D | ASN319 |
| site_id | AC5 |
| Number of Residues | 8 |
| Details | binding site for residue PG4 A 405 |
| Chain | Residue |
| A | ARG241 |
| A | GLU245 |
| A | ILE276 |
| A | ARG279 |
| A | GLU280 |
| A | MET303 |
| A | HOH517 |
| A | HOH537 |
| site_id | AC6 |
| Number of Residues | 14 |
| Details | binding site for residue FBY B 401 |
| Chain | Residue |
| B | ILE43 |
| B | VAL69 |
| B | LYS71 |
| B | PRO111 |
| B | MET131 |
| B | ASP132 |
| B | ARG133 |
| B | PHE134 |
| B | GLY135 |
| B | LEU184 |
| B | VAL196 |
| B | ASP197 |
| B | GOL408 |
| B | HOH505 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 B 402 |
| Chain | Residue |
| B | ARG241 |
| B | ARG279 |
| B | GOL405 |
| C | ARG89 |
| C | ARG203 |
| C | GOL405 |
| site_id | AC8 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 B 403 |
| Chain | Residue |
| B | LYS85 |
| B | ARG89 |
| site_id | AC9 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 B 404 |
| Chain | Residue |
| B | GLN95 |
| B | LYS98 |
| B | HIS171 |
| site_id | AD1 |
| Number of Residues | 8 |
| Details | binding site for residue GOL B 405 |
| Chain | Residue |
| B | TYR213 |
| B | ARG241 |
| B | ASP310 |
| B | TYR311 |
| B | SO4402 |
| B | HOH585 |
| C | ARG203 |
| C | GLU207 |
| site_id | AD2 |
| Number of Residues | 2 |
| Details | binding site for residue GOL B 406 |
| Chain | Residue |
| B | ARG148 |
| B | HIS258 |
| site_id | AD3 |
| Number of Residues | 7 |
| Details | binding site for residue GOL B 407 |
| Chain | Residue |
| B | CYS205 |
| B | ARG240 |
| B | HOH501 |
| B | HOH513 |
| B | HOH527 |
| B | HOH580 |
| B | HOH599 |
| site_id | AD4 |
| Number of Residues | 5 |
| Details | binding site for residue GOL B 408 |
| Chain | Residue |
| B | GLN45 |
| B | SER181 |
| B | ASN182 |
| B | ASP197 |
| B | FBY401 |
| site_id | AD5 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 C 401 |
| Chain | Residue |
| C | GLN95 |
| C | HIS171 |
| C | HOH529 |
| site_id | AD6 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 C 402 |
| Chain | Residue |
| C | ARG148 |
| C | HIS258 |
| site_id | AD7 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 C 403 |
| Chain | Residue |
| A | SO4402 |
| C | MET32 |
| C | TYR113 |
| C | HOH503 |
| C | HOH574 |
| C | HOH615 |
| site_id | AD8 |
| Number of Residues | 6 |
| Details | binding site for residue GOL C 404 |
| Chain | Residue |
| C | HIS169 |
| C | GLU170 |
| C | GLU172 |
| C | ARG240 |
| C | HOH522 |
| C | HOH586 |
| site_id | AD9 |
| Number of Residues | 5 |
| Details | binding site for residue GOL C 405 |
| Chain | Residue |
| B | ARG279 |
| B | SO4402 |
| C | ARG89 |
| C | ARG203 |
| C | HOH661 |
| site_id | AE1 |
| Number of Residues | 4 |
| Details | binding site for residue GOL C 406 |
| Chain | Residue |
| C | GLU280 |
| C | ASN281 |
| C | HOH564 |
| D | HOH587 |
| site_id | AE2 |
| Number of Residues | 6 |
| Details | binding site for residue GOL C 407 |
| Chain | Residue |
| C | ASN281 |
| C | ILE282 |
| C | GLU304 |
| C | LYS307 |
| C | HOH546 |
| C | GLU280 |
| site_id | AE3 |
| Number of Residues | 4 |
| Details | binding site for residue CL C 408 |
| Chain | Residue |
| C | ASP231 |
| C | SER239 |
| C | ARG241 |
| C | GLY242 |
| site_id | AE4 |
| Number of Residues | 14 |
| Details | binding site for residue FBY D 401 |
| Chain | Residue |
| D | ILE43 |
| D | VAL69 |
| D | LYS71 |
| D | PRO111 |
| D | MET131 |
| D | ASP132 |
| D | PHE134 |
| D | GLY135 |
| D | ASP137 |
| D | LEU184 |
| D | VAL196 |
| D | ASP197 |
| D | SO4406 |
| D | HOH513 |
| site_id | AE5 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 D 402 |
| Chain | Residue |
| C | PRO291 |
| C | ALA292 |
| C | HOH555 |
| D | SER150 |
| D | ARG151 |
| site_id | AE6 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 D 403 |
| Chain | Residue |
| D | GLN95 |
| D | HIS171 |
| D | GOL409 |
| D | HOH501 |
| site_id | AE7 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 D 404 |
| Chain | Residue |
| D | ARG148 |
| D | HIS258 |
| D | HOH526 |
| site_id | AE8 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 D 405 |
| Chain | Residue |
| D | ARG89 |
| D | HOH569 |
| site_id | AE9 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 D 406 |
| Chain | Residue |
| D | SER181 |
| D | ASN182 |
| D | ASP197 |
| D | FBY401 |
| site_id | AF1 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 D 407 |
| Chain | Residue |
| D | ASP177 |
| D | GLY223 |
| D | THR224 |
| D | HOH506 |
| site_id | AF2 |
| Number of Residues | 6 |
| Details | binding site for residue GOL D 408 |
| Chain | Residue |
| A | ARG203 |
| A | GLU207 |
| D | ARG241 |
| D | ASP310 |
| D | TYR311 |
| D | GOL413 |
| site_id | AF3 |
| Number of Residues | 4 |
| Details | binding site for residue GOL D 409 |
| Chain | Residue |
| D | ARG89 |
| D | GLU170 |
| D | HIS171 |
| D | SO4403 |
| site_id | AF4 |
| Number of Residues | 9 |
| Details | binding site for residue GOL D 410 |
| Chain | Residue |
| D | GLU245 |
| D | TYR249 |
| D | ARG279 |
| D | ILE282 |
| D | MET303 |
| D | VAL306 |
| D | CL416 |
| D | HOH502 |
| D | HOH533 |
| site_id | AF5 |
| Number of Residues | 5 |
| Details | binding site for residue GOL D 411 |
| Chain | Residue |
| D | HIS258 |
| D | LEU259 |
| D | PRO260 |
| D | LYS288 |
| D | HOH520 |
| site_id | AF6 |
| Number of Residues | 3 |
| Details | binding site for residue GOL D 412 |
| Chain | Residue |
| A | ARG89 |
| A | ARG203 |
| D | GOL413 |
| site_id | AF7 |
| Number of Residues | 6 |
| Details | binding site for residue GOL D 413 |
| Chain | Residue |
| A | ARG89 |
| D | ARG241 |
| D | ARG279 |
| D | GOL408 |
| D | GOL412 |
| D | HOH527 |
| site_id | AF8 |
| Number of Residues | 6 |
| Details | binding site for residue GOL D 414 |
| Chain | Residue |
| A | LYS85 |
| A | GLN88 |
| A | LYS92 |
| D | LEU308 |
| D | ASP310 |
| D | GLU313 |
| site_id | AF9 |
| Number of Residues | 2 |
| Details | binding site for residue ACT D 415 |
| Chain | Residue |
| D | ASP273 |
| D | ARG277 |
| site_id | AG1 |
| Number of Residues | 6 |
| Details | binding site for residue CL D 416 |
| Chain | Residue |
| D | TYR278 |
| D | ARG279 |
| D | LEU285 |
| D | MET303 |
| D | GOL410 |
| D | HOH531 |
Functional Information from PROSITE/UniProt
| site_id | PS00107 |
| Number of Residues | 29 |
| Details | PROTEIN_KINASE_ATP Protein kinases ATP-binding region signature. IGQGGFGCIYlAdmnssesvgsdap.....CVVK |
| Chain | Residue | Details |
| A | ILE43-LYS71 |
| site_id | PS00108 |
| Number of Residues | 13 |
| Details | PROTEIN_KINASE_ST Serine/Threonine protein kinases active-site signature. YvHgDIKasNLLL |
| Chain | Residue | Details |
| A | TYR173-LEU185 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | ACT_SITE: Proton acceptor => ECO:0000255|PROSITE-ProRule:PRU00159, ECO:0000255|PROSITE-ProRule:PRU10027 |
| Chain | Residue | Details |
| A | ASP177 | |
| B | ASP177 | |
| C | ASP177 | |
| D | ASP177 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00159 |
| Chain | Residue | Details |
| A | ILE43 | |
| A | LYS71 | |
| B | ILE43 | |
| B | LYS71 | |
| C | ILE43 | |
| C | LYS71 | |
| D | ILE43 | |
| D | LYS71 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine; by PLK3 => ECO:0000269|PubMed:19103756, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER342 | |
| B | SER342 | |
| C | SER342 | |
| D | SER342 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphothreonine; by autocatalysis => ECO:0000269|PubMed:11883897 |
| Chain | Residue | Details |
| A | THR355 | |
| B | THR355 | |
| C | THR355 | |
| D | THR355 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 8 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| A | LYS71 | |
| B | LYS71 | |
| C | LYS71 | |
| D | LYS71 |
