2YBE
The structure of the fully closed conformation of human PGK in complex with L-ADP, 3PG and the TSA aluminium tetrafluoride at 2.0 A resolution
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 pyruvate decarboxylation to acetyl-CoA |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG A 1417 |
| Chain | Residue |
| A | ASP374 |
| A | LA81419 |
| A | ALF1420 |
| A | HOH2112 |
| A | HOH2115 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE CL A 1418 |
| Chain | Residue |
| A | ARG65 |
| A | LYS215 |
| A | ALA217 |
| A | ASP218 |
| site_id | AC3 |
| Number of Residues | 22 |
| Details | BINDING SITE FOR RESIDUE LA8 A 1419 |
| Chain | Residue |
| A | GLY213 |
| A | ALA214 |
| A | LYS215 |
| A | LYS219 |
| A | GLY238 |
| A | ASN336 |
| A | PRO338 |
| A | GLY340 |
| A | VAL341 |
| A | PHE342 |
| A | GLU343 |
| A | GLY371 |
| A | GLY372 |
| A | GLY373 |
| A | ASP374 |
| A | THR375 |
| A | MG1417 |
| A | ALF1420 |
| A | HOH2110 |
| A | HOH2111 |
| A | HOH2112 |
| A | HOH2113 |
| site_id | AC4 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE ALF A 1420 |
| Chain | Residue |
| A | ARG38 |
| A | LYS215 |
| A | LYS219 |
| A | GLY372 |
| A | GLY373 |
| A | GLY395 |
| A | GLY396 |
| A | MG1417 |
| A | LA81419 |
| A | 3PG1421 |
| A | HOH2047 |
| A | HOH2112 |
| A | HOH2114 |
| A | HOH2115 |
| site_id | AC5 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE 3PG A 1421 |
| Chain | Residue |
| A | ASP23 |
| A | ASN25 |
| A | ARG38 |
| A | HIS62 |
| A | ARG65 |
| A | ARG122 |
| A | GLY166 |
| A | THR167 |
| A | ARG170 |
| A | LYS215 |
| A | ALF1420 |
| A | HOH2114 |
| A | HOH2115 |
| A | HOH2116 |
Functional Information from PROSITE/UniProt
| site_id | PS00111 |
| Number of Residues | 11 |
| Details | PGLYCERATE_KINASE Phosphoglycerate kinase signature. RVVMRvDfNVP |
| Chain | Residue | Details |
| A | ARG17-PRO27 |
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 | VAL22 | |
| A | PHE24 | |
| A | GLN37 | |
| A | LEU121 | |
| A | HIS169 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 14 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:Q7SIB7 |
| Chain | Residue | Details |
| A | ASP23 | |
| A | GLY238 | |
| A | GLY312 | |
| A | GLU343 | |
| A | ASP374 | |
| A | THR375 | |
| A | ASN25 | |
| A | ARG38 | |
| A | HIS62 | |
| A | ARG65 | |
| A | ARG122 | |
| A | ARG170 | |
| A | LYS215 | |
| A | LYS219 |
| 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 | SER61 | |
| A | GLY64 |
| 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 | GLY213 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:18463139, ECO:0007744|PDB:3C3A |
| Chain | Residue | Details |
| A | ALA214 | |
| A | ASP218 |
| 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 | ALA217 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:18463139, ECO:0007744|PDB:3C3B |
| Chain | Residue | Details |
| A | GLY237 | |
| A | GLY337 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:18463139, ECO:0007744|PDB:3C3C |
| Chain | Residue | Details |
| A | VAL339 | |
| A | PHE342 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER1 | |
| A | SER3 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:P09411 |
| Chain | Residue | Details |
| A | LYS5 | |
| A | LYS190 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 7 |
| Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
| Chain | Residue | Details |
| A | LYS10 | |
| A | LYS74 | |
| A | LYS85 | |
| A | LYS145 | |
| A | LYS198 | |
| A | LYS266 | |
| A | LYS290 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 1 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P09411 |
| Chain | Residue | Details |
| A | LYS47 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P09411 |
| Chain | Residue | Details |
| A | TYR75 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P09411 |
| Chain | Residue | Details |
| A | LYS90 | |
| A | LYS360 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 1 |
| Details | MOD_RES: N6-acetyllysine; alternate => ECO:0007744|PubMed:19608861 |
| Chain | Residue | Details |
| A | LYS96 |
| site_id | SWS_FT_FI16 |
| Number of Residues | 1 |
| Details | MOD_RES: N6-malonyllysine; alternate => ECO:0000269|PubMed:21908771 |
| Chain | Residue | Details |
| A | LYS130 |
| site_id | SWS_FT_FI17 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphotyrosine => ECO:0007744|PubMed:15592455 |
| Chain | Residue | Details |
| A | TYR195 |
| 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 | SER202 |
| site_id | SWS_FT_FI19 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-(2-hydroxyisobutyryl)lysine => ECO:0000269|PubMed:29775581 |
| Chain | Residue | Details |
| A | LYS215 | |
| A | LYS322 |
| site_id | SWS_FT_FI20 |
| Number of Residues | 1 |
| Details | MOD_RES: N6-(2-hydroxyisobutyryl)lysine => ECO:0000269|PubMed:29192674 |
| Chain | Residue | Details |
| A | LYS219 |
