5VBI
Crystal Structure of the R515W 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 | 0005980 | biological_process | glycogen catabolic 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, Leloir pathway |
| 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 | 0005980 | biological_process | glycogen catabolic 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, Leloir pathway |
| 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 | 6 |
| Details | binding site for residue SO4 A 601 |
| Chain | Residue |
| A | ASN179 |
| A | LYS470 |
| A | ARG491 |
| A | HOH875 |
| A | HOH1008 |
| A | HOH1027 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 A 602 |
| Chain | Residue |
| A | HOH906 |
| A | HOH927 |
| A | ARG217 |
| A | ARG221 |
| A | PRO244 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 A 603 |
| Chain | Residue |
| A | SER505 |
| A | GLY506 |
| A | HOH706 |
| A | HOH874 |
| A | HOH1107 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | binding site for residue MG A 604 |
| Chain | Residue |
| A | SEP117 |
| A | ASP288 |
| A | ASP290 |
| A | ASP292 |
| A | HOH762 |
| A | HOH899 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | binding site for residue GOL A 605 |
| Chain | Residue |
| A | ARG343 |
| A | ASP496 |
| A | LYS523 |
| A | HOH847 |
| A | HOH933 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | binding site for residue GOL A 606 |
| Chain | Residue |
| A | THR19 |
| A | GLY358 |
| A | TRP359 |
| A | HOH720 |
| A | HOH832 |
| A | HOH1119 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | binding site for residue GOL A 607 |
| Chain | Residue |
| A | PRO244 |
| A | ALA245 |
| A | HOH705 |
| A | HOH906 |
| A | HOH1010 |
| site_id | AC8 |
| Number of Residues | 7 |
| Details | binding site for residue GOL A 608 |
| Chain | Residue |
| A | MET442 |
| A | ASN473 |
| A | ASN487 |
| A | GLY489 |
| A | LEU490 |
| A | HOH707 |
| A | HOH717 |
| site_id | AC9 |
| Number of Residues | 9 |
| Details | binding site for residue GOL A 609 |
| Chain | Residue |
| A | ASN305 |
| A | PRO306 |
| A | GLU377 |
| A | PHE425 |
| A | THR426 |
| A | ARG427 |
| A | THR562 |
| A | HOH719 |
| A | HOH739 |
| site_id | AD1 |
| Number of Residues | 8 |
| Details | binding site for residue GOL A 610 |
| Chain | Residue |
| A | GLU377 |
| A | ARG427 |
| A | ARG503 |
| A | TRP515 |
| A | TYR517 |
| A | HOH780 |
| A | HOH874 |
| A | HOH1163 |
| site_id | AD2 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 B 601 |
| Chain | Residue |
| B | ARG217 |
| B | ARG221 |
| B | ARG221 |
| B | PRO244 |
| B | ASN246 |
| B | HOH714 |
| site_id | AD3 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 B 602 |
| Chain | Residue |
| B | ALA314 |
| B | ALA315 |
| B | PHE318 |
| B | HOH737 |
| B | HOH902 |
| site_id | AD4 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 603 |
| Chain | Residue |
| B | SEP117 |
| B | ASP288 |
| B | ASP290 |
| B | ASP292 |
| B | HOH761 |
| B | HOH873 |
| site_id | AD5 |
| Number of Residues | 7 |
| Details | binding site for residue GOL B 604 |
| Chain | Residue |
| B | ILE106 |
| B | VAL189 |
| B | GLU193 |
| B | ALA194 |
| B | HOH772 |
| B | HOH819 |
| B | HOH835 |
| site_id | AD6 |
| Number of Residues | 7 |
| Details | binding site for residue GOL B 605 |
| Chain | Residue |
| B | THR19 |
| B | GLY358 |
| B | TRP359 |
| B | HOH711 |
| B | HOH717 |
| B | HOH756 |
| B | HOH857 |
| site_id | AD7 |
| Number of Residues | 4 |
| Details | binding site for residue GOL B 606 |
| Chain | Residue |
| B | ARG503 |
| B | LEU504 |
| B | SER505 |
| B | GLY506 |
| site_id | AD8 |
| Number of Residues | 8 |
| Details | binding site for residue GOL B 607 |
| Chain | Residue |
| B | ARG422 |
| B | PHE424 |
| B | PHE425 |
| B | HOH782 |
| B | HOH789 |
| B | HOH871 |
| B | PHE303 |
| B | ASN305 |
| site_id | AD9 |
| Number of Residues | 6 |
| Details | binding site for residue GOL B 608 |
| Chain | Residue |
| B | ASN179 |
| B | LYS470 |
| B | ARG491 |
| B | ILE493 |
| B | HOH716 |
| B | HOH752 |
| site_id | AE1 |
| Number of Residues | 2 |
| Details | binding site for residue GOL B 609 |
| Chain | Residue |
| B | ARG343 |
| B | ASP496 |
| site_id | AE2 |
| Number of Residues | 6 |
| Details | binding site for residue GOL B 610 |
| Chain | Residue |
| B | GLU377 |
| B | ARG427 |
| B | ARG503 |
| B | TRP515 |
| B | TYR517 |
| B | HOH758 |
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 | Active site: {"description":"Phosphoserine intermediate","evidences":[{"source":"PubMed","id":"25288802","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 12 |
| Details | Binding site: {"evidences":[{"source":"UniProtKB","id":"P00949","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | Binding site: {"description":"via phosphate groupe","evidences":[{"source":"PubMed","id":"25288802","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 6 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"26972339","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"5EPC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F9C","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N-acetylmethionine","evidences":[{"source":"PubMed","id":"21406692","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"Q9D0F9","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"25288802","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19690332","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"21406692","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI9 |
| Number of Residues | 12 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P38652","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI11 |
| Number of Residues | 10 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI12 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"Q9D0F9","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI13 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"Q9D0F9","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI14 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"Q9D0F9","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI15 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphothreonine; by PAK1","evidences":[{"source":"PubMed","id":"15378030","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
