5VIN
Crystal Structure of the R515Q 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 | 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 | 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 | 4 |
| Details | binding site for residue SO4 A 601 |
| Chain | Residue |
| A | THR19 |
| A | GLY358 |
| A | TRP359 |
| A | HOH712 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 A 602 |
| Chain | Residue |
| A | HIS118 |
| A | ARG293 |
| A | ARG427 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 A 603 |
| Chain | Residue |
| A | LYS68 |
| A | GLU69 |
| A | GLU255 |
| A | TYR66 |
| A | MET67 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 A 604 |
| Chain | Residue |
| A | GLY259 |
| A | HIS260 |
| A | HIS261 |
| A | TYR268 |
| site_id | AC5 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 A 605 |
| Chain | Residue |
| A | SER31 |
| A | SER32 |
| A | ALA33 |
| site_id | AC6 |
| Number of Residues | 1 |
| Details | binding site for residue SO4 A 606 |
| Chain | Residue |
| A | ARG555 |
| site_id | AC7 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 A 607 |
| Chain | Residue |
| A | PRO123 |
| A | ASN124 |
| A | GLY125 |
| site_id | AC8 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 A 608 |
| Chain | Residue |
| A | PRO244 |
| A | ALA245 |
| site_id | AC9 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 A 609 |
| Chain | Residue |
| A | LYS470 |
| A | ARG491 |
| site_id | AD1 |
| Number of Residues | 4 |
| Details | binding site for residue GOL A 610 |
| Chain | Residue |
| A | ARG217 |
| A | ARG221 |
| A | PRO244 |
| A | ASN246 |
| site_id | AD2 |
| Number of Residues | 2 |
| Details | binding site for residue GOL A 611 |
| Chain | Residue |
| A | ARG85 |
| A | HOH728 |
| site_id | AD3 |
| Number of Residues | 1 |
| Details | binding site for residue GOL A 612 |
| Chain | Residue |
| A | HIS260 |
| site_id | AD4 |
| Number of Residues | 4 |
| Details | binding site for residue CO A 614 |
| Chain | Residue |
| A | SER117 |
| A | ASP288 |
| A | ASP290 |
| A | ASP292 |
| site_id | AD5 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 B 601 |
| Chain | Residue |
| B | ARG427 |
| B | GOL606 |
| site_id | AD6 |
| Number of Residues | 7 |
| Details | binding site for residue SO4 B 602 |
| Chain | Residue |
| B | THR19 |
| B | SER20 |
| B | GLY358 |
| B | TRP359 |
| B | LYS389 |
| B | HOH702 |
| B | HOH716 |
| site_id | AD7 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 B 603 |
| Chain | Residue |
| A | SER-1 |
| A | ASN0 |
| B | SER206 |
| site_id | AD8 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 B 604 |
| Chain | Residue |
| B | PRO244 |
| B | ALA245 |
| site_id | AD9 |
| Number of Residues | 2 |
| Details | binding site for residue GOL B 605 |
| Chain | Residue |
| B | GLY18 |
| B | THR19 |
| site_id | AE1 |
| Number of Residues | 4 |
| Details | binding site for residue GOL B 606 |
| Chain | Residue |
| B | ARG503 |
| B | SER505 |
| B | THR507 |
| B | SO4601 |
| site_id | AE2 |
| Number of Residues | 4 |
| Details | binding site for residue CO B 607 |
| Chain | Residue |
| B | SER117 |
| 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 | SER117 | |
| B | SER117 |
| 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 | SER117 | |
| B | SER117 |
| 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 | SER117 | |
| B | SER117 |
| 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 |
