5VG7
Crystal Structure of the R503Q 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 | 0071704 | biological_process | obsolete organic substance metabolic process |
| 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 | 0071704 | biological_process | obsolete organic substance metabolic process |
| 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 | 6 |
| Details | binding site for residue MG A 601 |
| Chain | Residue |
| A | SEP117 |
| A | ASP288 |
| A | ASP290 |
| A | ASP292 |
| A | HOH748 |
| A | HOH897 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 A 602 |
| Chain | Residue |
| A | ASN246 |
| A | HOH713 |
| A | ARG217 |
| A | ARG221 |
| A | PRO244 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 A 603 |
| Chain | Residue |
| A | ASN179 |
| A | LYS470 |
| A | ARG491 |
| A | HOH726 |
| A | HOH895 |
| A | HOH930 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 A 604 |
| Chain | Residue |
| A | GLN324 |
| B | ALA314 |
| B | ALA315 |
| B | THR348 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 A 605 |
| Chain | Residue |
| A | THR19 |
| A | GLY358 |
| A | TRP359 |
| A | HOH721 |
| A | HOH961 |
| A | HOH999 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 A 606 |
| Chain | Residue |
| A | GLU187 |
| A | HOH898 |
| site_id | AC7 |
| Number of Residues | 1 |
| Details | binding site for residue SO4 A 607 |
| Chain | Residue |
| A | HIS260 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 A 608 |
| Chain | Residue |
| A | SER505 |
| A | GLY506 |
| A | ARG515 |
| A | HOH760 |
| site_id | AC9 |
| Number of Residues | 7 |
| Details | binding site for residue SO4 A 609 |
| Chain | Residue |
| A | GLU432 |
| A | VAL433 |
| A | GLU434 |
| A | ARG555 |
| A | HOH704 |
| A | HOH818 |
| A | HOH988 |
| site_id | AD1 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 A 610 |
| Chain | Residue |
| A | LYS299 |
| A | HIS300 |
| A | HOH929 |
| site_id | AD2 |
| Number of Residues | 7 |
| Details | binding site for residue SO4 A 611 |
| Chain | Residue |
| A | TYR66 |
| A | MET67 |
| A | LYS68 |
| A | GLU69 |
| A | GLU255 |
| A | HOH951 |
| A | HOH1005 |
| site_id | AD3 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 A 612 |
| Chain | Residue |
| A | PRO244 |
| A | ALA245 |
| A | HOH954 |
| site_id | AD4 |
| Number of Residues | 4 |
| Details | binding site for residue GOL A 613 |
| Chain | Residue |
| A | ARG343 |
| A | ASP496 |
| A | GLY497 |
| A | HOH970 |
| site_id | AD5 |
| Number of Residues | 5 |
| Details | binding site for residue GOL A 614 |
| Chain | Residue |
| A | THR326 |
| A | ARG329 |
| A | HOH797 |
| B | GLN325 |
| B | ARG329 |
| site_id | AD6 |
| Number of Residues | 8 |
| Details | binding site for residue GOL A 615 |
| Chain | Residue |
| A | PHE303 |
| A | ASN305 |
| A | ARG422 |
| A | PHE424 |
| A | PHE425 |
| A | PRO532 |
| A | HOH813 |
| A | HOH853 |
| site_id | AD7 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 601 |
| Chain | Residue |
| B | SER117 |
| B | ASP288 |
| B | ASP290 |
| B | ASP292 |
| B | HOH724 |
| B | HOH823 |
| site_id | AD8 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 B 602 |
| Chain | Residue |
| B | SER505 |
| B | GLY506 |
| B | ARG515 |
| site_id | AD9 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 B 603 |
| Chain | Residue |
| B | ARG221 |
| B | ARG221 |
| B | ASN246 |
| B | HIS281 |
| B | HOH908 |
| B | HOH908 |
| site_id | AE1 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 B 604 |
| Chain | Residue |
| B | ARG85 |
| B | ILE106 |
| B | HOH707 |
| B | HOH806 |
| site_id | AE2 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 B 605 |
| Chain | Residue |
| B | ARG293 |
| B | SER378 |
| B | ARG427 |
| B | HOH717 |
| B | HOH920 |
| site_id | AE3 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 B 606 |
| Chain | Residue |
| B | HOH703 |
| B | ASN179 |
| B | GLU354 |
| B | LYS470 |
| B | ARG491 |
| site_id | AE4 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 B 607 |
| Chain | Residue |
| B | GLN41 |
| B | SER45 |
| B | ARG52 |
| B | ASN81 |
| site_id | AE5 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 B 608 |
| Chain | Residue |
| B | GLU432 |
| B | VAL433 |
| B | GLU434 |
| B | ARG555 |
| site_id | AE6 |
| Number of Residues | 5 |
| Details | binding site for residue GOL B 609 |
| Chain | Residue |
| B | ASP204 |
| B | SER319 |
| B | GLN324 |
| B | THR404 |
| B | HOH790 |
| site_id | AE7 |
| Number of Residues | 4 |
| Details | binding site for residue GOL B 610 |
| Chain | Residue |
| B | GLY358 |
| B | TRP359 |
| B | GLU376 |
| B | HOH826 |
Functional Information from PROSITE/UniProt
| site_id | PS00710 |
| Number of Residues | 10 |
| Details | PGM_PMM Phosphoglucomutase and phosphomannomutase phosphoserine signature. GIiLTASHNP |
| Chain | Residue | Details |
| B | GLY111-PRO120 | |
| A | GLY111-PRO120 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 1 |
| Details | ACT_SITE: Phosphoserine intermediate => ECO:0000269|PubMed:25288802 |
| Chain | Residue | Details |
| B | SER117 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:P00949 |
| Chain | Residue | Details |
| B | ARG23 | |
| B | ARG293 | |
| B | THR357 | |
| B | GLU376 | |
| B | SER378 | |
| B | LYS389 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 1 |
| Details | BINDING: via phosphate groupe => ECO:0000269|PubMed:25288802 |
| Chain | Residue | Details |
| B | SER117 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 3 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:26972339, ECO:0007744|PDB:5EPC, ECO:0007744|PDB:5F9C |
| Chain | Residue | Details |
| B | ASP288 | |
| B | ASP290 | |
| B | ASP292 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 1 |
| Details | MOD_RES: N-acetylmethionine => ECO:0007744|PubMed:22814378 |
| Chain | Residue | Details |
| B | MET1 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 1 |
| Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
| Chain | Residue | Details |
| B | LYS16 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q9D0F9 |
| Chain | Residue | Details |
| B | THR115 | |
| B | THR507 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:25288802, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692 |
| Chain | Residue | Details |
| B | SER117 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 6 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P38652 |
| Chain | Residue | Details |
| B | SER134 | |
| B | SER213 | |
| B | SER369 | |
| B | SER477 | |
| B | SER485 | |
| B | SER541 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| B | THR185 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 5 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| B | SER201 | |
| B | SER206 | |
| B | SER378 | |
| B | SER505 | |
| B | SER509 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 1 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:Q9D0F9 |
| Chain | Residue | Details |
| B | LYS349 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:Q9D0F9 |
| Chain | Residue | Details |
| B | TYR353 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 1 |
| Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:Q9D0F9 |
| Chain | Residue | Details |
| B | LYS419 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphothreonine; by PAK1 => ECO:0000269|PubMed:15378030 |
| Chain | Residue | Details |
| B | THR467 |
