4AXX
The catalytically active fully closed conformation of human phosphoglycerate kinase in complex with ADP 3-phosphoglycerate and beryllium trifluoride
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| A | 0004618 | molecular_function | phosphoglycerate kinase activity |
| A | 0004674 | molecular_function | protein serine/threonine kinase activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005524 | molecular_function | ATP binding |
| A | 0005615 | cellular_component | extracellular space |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005739 | cellular_component | mitochondrion |
| A | 0005759 | cellular_component | mitochondrial matrix |
| A | 0005829 | cellular_component | cytosol |
| A | 0006094 | biological_process | gluconeogenesis |
| A | 0006096 | biological_process | glycolytic process |
| A | 0016020 | cellular_component | membrane |
| A | 0016301 | molecular_function | kinase activity |
| A | 0016525 | biological_process | negative regulation of angiogenesis |
| A | 0016740 | molecular_function | transferase activity |
| A | 0030855 | biological_process | epithelial cell differentiation |
| A | 0031639 | biological_process | plasminogen activation |
| A | 0043531 | molecular_function | ADP binding |
| A | 0044325 | molecular_function | transmembrane transporter binding |
| A | 0045121 | cellular_component | membrane raft |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0047134 | molecular_function | protein-disulfide reductase [NAD(P)H] activity |
| A | 0061621 | biological_process | canonical glycolysis |
| A | 0070062 | cellular_component | extracellular exosome |
| A | 0071456 | biological_process | cellular response to hypoxia |
| A | 0106310 | molecular_function | protein serine kinase activity |
| A | 0160218 | biological_process | negative regulation of acetyl-CoA biosynthetic process from pyruvate |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG A 1418 |
| Chain | Residue |
| A | ASP375 |
| A | ADP1420 |
| A | BEF1422 |
| A | HOH2236 |
| A | HOH2388 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE CL A 1419 |
| Chain | Residue |
| A | ARG66 |
| A | LYS216 |
| A | ASP219 |
| site_id | AC3 |
| Number of Residues | 29 |
| Details | BINDING SITE FOR RESIDUE ADP A 1420 |
| Chain | Residue |
| A | ALA215 |
| A | LYS216 |
| A | LYS220 |
| A | GLY238 |
| A | GLY239 |
| A | PHE242 |
| A | LEU257 |
| A | GLY313 |
| A | LEU314 |
| A | ASN337 |
| A | PRO339 |
| A | GLY341 |
| A | VAL342 |
| A | GLU344 |
| A | GLY373 |
| A | GLY374 |
| A | ASP375 |
| A | THR376 |
| A | MG1418 |
| A | BEF1422 |
| A | HOH2235 |
| A | HOH2236 |
| A | HOH2286 |
| A | HOH2340 |
| A | HOH2386 |
| A | HOH2388 |
| A | HOH2418 |
| A | HOH2419 |
| A | GLY214 |
| site_id | AC4 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE 3PG A 1421 |
| Chain | Residue |
| A | ASP24 |
| A | ASN26 |
| A | ARG39 |
| A | HIS63 |
| A | ARG66 |
| A | ARG123 |
| A | GLY167 |
| A | THR168 |
| A | ARG171 |
| A | LYS216 |
| A | BEF1422 |
| A | HOH2051 |
| A | HOH2167 |
| A | HOH2193 |
| A | HOH2196 |
| A | HOH2388 |
| site_id | AC5 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE BEF A 1422 |
| Chain | Residue |
| A | ARG39 |
| A | LYS216 |
| A | LYS220 |
| A | GLY373 |
| A | GLY374 |
| A | GLY396 |
| A | GLY397 |
| A | MG1418 |
| A | ADP1420 |
| A | 3PG1421 |
| A | HOH2196 |
| A | HOH2236 |
| A | HOH2388 |
Functional Information from PROSITE/UniProt
| site_id | PS00111 |
| Number of Residues | 11 |
| Details | PGLYCERATE_KINASE Phosphoglycerate kinase signature. RVVMRvDfNVP |
| Chain | Residue | Details |
| A | ARG18-PRO28 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 5 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:18463139, ECO:0007744|PDB:3C39, ECO:0007744|PDB:3C3A, ECO:0007744|PDB:3C3C |
| Chain | Residue | Details |
| A | VAL23 | |
| A | PHE25 | |
| A | GLN38 | |
| A | LEU122 | |
| A | HIS170 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 14 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:Q7SIB7 |
| Chain | Residue | Details |
| A | ASP24 | |
| A | GLY239 | |
| A | GLY313 | |
| A | GLU344 | |
| A | ASP375 | |
| A | THR376 | |
| A | ASN26 | |
| A | ARG39 | |
| A | HIS63 | |
| A | ARG66 | |
| A | ARG123 | |
| A | ARG171 | |
| A | LYS216 | |
| A | LYS220 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:18463139, ECO:0007744|PDB:3C39, ECO:0007744|PDB:3C3C |
| Chain | Residue | Details |
| A | SER62 | |
| A | GLY65 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 1 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:18463139, ECO:0007744|PDB:3C3B, ECO:0007744|PDB:3C3C |
| Chain | Residue | Details |
| A | GLY214 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:18463139, ECO:0007744|PDB:3C3A |
| Chain | Residue | Details |
| A | ALA215 | |
| A | ASP219 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 1 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:18463139, ECO:0007744|PDB:3C3A, ECO:0007744|PDB:3C3C |
| Chain | Residue | Details |
| A | ALA218 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:18463139, ECO:0007744|PDB:3C3B |
| Chain | Residue | Details |
| A | GLY238 | |
| A | GLY338 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:18463139, ECO:0007744|PDB:3C3C |
| Chain | Residue | Details |
| A | VAL340 | |
| A | PHE343 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER2 | |
| A | SER4 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:P09411 |
| Chain | Residue | Details |
| A | LYS6 | |
| A | LYS191 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 7 |
| Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
| Chain | Residue | Details |
| A | LYS11 | |
| A | LYS75 | |
| A | LYS86 | |
| A | LYS146 | |
| A | LYS199 | |
| A | LYS267 | |
| A | LYS291 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 1 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P09411 |
| Chain | Residue | Details |
| A | LYS48 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P09411 |
| Chain | Residue | Details |
| A | TYR76 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P09411 |
| Chain | Residue | Details |
| A | LYS91 | |
| A | LYS361 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 1 |
| Details | MOD_RES: N6-acetyllysine; alternate => ECO:0007744|PubMed:19608861 |
| Chain | Residue | Details |
| A | LYS97 |
| site_id | SWS_FT_FI16 |
| Number of Residues | 1 |
| Details | MOD_RES: N6-malonyllysine; alternate => ECO:0000269|PubMed:21908771 |
| Chain | Residue | Details |
| A | LYS131 |
| site_id | SWS_FT_FI17 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphotyrosine => ECO:0007744|PubMed:15592455 |
| Chain | Residue | Details |
| A | TYR196 |
| site_id | SWS_FT_FI18 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine; by MAPK1 => ECO:0000269|PubMed:26942675, ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| A | SER203 |
| site_id | SWS_FT_FI19 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-(2-hydroxyisobutyryl)lysine => ECO:0000269|PubMed:29775581 |
| Chain | Residue | Details |
| A | LYS216 | |
| A | LYS323 |
| site_id | SWS_FT_FI20 |
| Number of Residues | 1 |
| Details | MOD_RES: N6-(2-hydroxyisobutyryl)lysine => ECO:0000269|PubMed:29192674 |
| Chain | Residue | Details |
| A | LYS220 |
