5JN5
Crystal structure of the D263Y missense variant of human PGM1
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0004614 | molecular_function | phosphoglucomutase activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005576 | cellular_component | extracellular region |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0005975 | biological_process | carbohydrate metabolic process |
| A | 0006006 | biological_process | glucose metabolic process |
| A | 0006094 | biological_process | gluconeogenesis |
| A | 0006096 | biological_process | glycolytic process |
| A | 0016853 | molecular_function | isomerase activity |
| A | 0016868 | molecular_function | intramolecular phosphotransferase activity |
| A | 0033499 | biological_process | galactose catabolic process via UDP-galactose |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0070062 | cellular_component | extracellular exosome |
| A | 1904724 | cellular_component | tertiary granule lumen |
| A | 1904813 | cellular_component | ficolin-1-rich granule lumen |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0004614 | molecular_function | phosphoglucomutase activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005576 | cellular_component | extracellular region |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0005975 | biological_process | carbohydrate metabolic process |
| B | 0006006 | biological_process | glucose metabolic process |
| B | 0006094 | biological_process | gluconeogenesis |
| B | 0006096 | biological_process | glycolytic process |
| B | 0016853 | molecular_function | isomerase activity |
| B | 0016868 | molecular_function | intramolecular phosphotransferase activity |
| B | 0033499 | biological_process | galactose catabolic process via UDP-galactose |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0070062 | cellular_component | extracellular exosome |
| B | 1904724 | cellular_component | tertiary granule lumen |
| B | 1904813 | cellular_component | ficolin-1-rich granule lumen |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 8 |
| Details | binding site for residue SO4 A 601 |
| Chain | Residue |
| A | ARG503 |
| A | SER505 |
| A | GLY506 |
| A | ARG515 |
| A | HOH1145 |
| A | HOH1168 |
| A | HOH1186 |
| A | HOH1192 |
| site_id | AC2 |
| Number of Residues | 8 |
| Details | binding site for residue SO4 A 602 |
| Chain | Residue |
| A | TYR66 |
| A | MET67 |
| A | LYS68 |
| A | GLU69 |
| A | GLU255 |
| A | HOH965 |
| A | HOH1053 |
| A | PHE65 |
| site_id | AC3 |
| Number of Residues | 7 |
| Details | binding site for residue SO4 A 603 |
| Chain | Residue |
| A | ARG217 |
| A | ARG221 |
| A | PRO244 |
| A | ASN246 |
| A | HOH1015 |
| A | HOH1040 |
| A | HOH1135 |
| site_id | AC4 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 A 604 |
| Chain | Residue |
| A | HIS260 |
| A | HIS261 |
| A | HOH999 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | binding site for residue CA A 605 |
| Chain | Residue |
| A | SEP117 |
| A | ASP288 |
| A | ASP290 |
| A | ASP292 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 B 601 |
| Chain | Residue |
| B | ARG503 |
| B | SER505 |
| B | GLY506 |
| B | ARG515 |
| B | HOH922 |
| B | HOH1007 |
| site_id | AC7 |
| Number of Residues | 10 |
| Details | binding site for residue SO4 B 602 |
| Chain | Residue |
| B | ARG221 |
| B | ARG221 |
| B | PRO244 |
| B | ASN246 |
| B | THR275 |
| B | HIS281 |
| B | HOH918 |
| B | HOH934 |
| B | HOH1037 |
| B | HOH1083 |
| site_id | AC8 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 B 603 |
| Chain | Residue |
| B | HIS260 |
| B | HIS261 |
| B | HOH1060 |
| site_id | AC9 |
| Number of Residues | 4 |
| Details | binding site for residue CA B 604 |
| Chain | Residue |
| B | SEP117 |
| B | ASP288 |
| B | ASP290 |
| B | ASP292 |
Functional Information from PROSITE/UniProt
| site_id | PS00710 |
| Number of Residues | 10 |
| Details | PGM_PMM Phosphoglucomutase and phosphomannomutase phosphoserine signature. GIiLTASHNP |
| Chain | Residue | Details |
| A | GLY111-PRO120 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | ACT_SITE: Phosphoserine intermediate => ECO:0000269|PubMed:25288802 |
| Chain | Residue | Details |
| A | SEP117 | |
| B | SEP117 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:P00949 |
| Chain | Residue | Details |
| A | ARG23 | |
| B | GLU376 | |
| B | SER378 | |
| B | LYS389 | |
| A | ARG293 | |
| A | THR357 | |
| A | GLU376 | |
| A | SER378 | |
| A | LYS389 | |
| B | ARG23 | |
| B | ARG293 | |
| B | THR357 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | BINDING: via phosphate groupe => ECO:0000269|PubMed:25288802 |
| Chain | Residue | Details |
| A | SEP117 | |
| B | SEP117 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:26972339, ECO:0007744|PDB:5EPC, ECO:0007744|PDB:5F9C |
| Chain | Residue | Details |
| A | ASP288 | |
| A | ASP290 | |
| A | ASP292 | |
| B | ASP288 | |
| B | ASP290 | |
| B | ASP292 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | MOD_RES: N-acetylmethionine => ECO:0007744|PubMed:22814378 |
| Chain | Residue | Details |
| A | MET1 | |
| B | MET1 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
| Chain | Residue | Details |
| A | LYS16 | |
| B | LYS16 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q9D0F9 |
| Chain | Residue | Details |
| A | THR115 | |
| A | THR507 | |
| B | THR115 | |
| B | THR507 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:25288802, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692 |
| Chain | Residue | Details |
| A | SEP117 | |
| B | SEP117 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 12 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P38652 |
| Chain | Residue | Details |
| A | SER134 | |
| B | SER477 | |
| B | SER485 | |
| B | SER541 | |
| A | SER213 | |
| A | SER369 | |
| A | SER477 | |
| A | SER485 | |
| A | SER541 | |
| B | SER134 | |
| B | SER213 | |
| B | SER369 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| A | THR185 | |
| B | THR185 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 10 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| A | SER201 | |
| B | SER509 | |
| A | SER206 | |
| A | SER378 | |
| A | SER505 | |
| A | SER509 | |
| B | SER201 | |
| B | SER206 | |
| B | SER378 | |
| B | SER505 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:Q9D0F9 |
| Chain | Residue | Details |
| A | LYS349 | |
| B | LYS349 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:Q9D0F9 |
| Chain | Residue | Details |
| A | TYR353 | |
| B | TYR353 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:Q9D0F9 |
| Chain | Residue | Details |
| A | LYS419 | |
| B | LYS419 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine; by PAK1 => ECO:0000269|PubMed:15378030 |
| Chain | Residue | Details |
| A | THR467 | |
| B | THR467 |
