3PYM
Structure of GAPDH 3 from S.cerevisiae at 2.0 A resolution
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003723 | molecular_function | RNA binding |
| A | 0003729 | molecular_function | mRNA binding |
| A | 0004365 | molecular_function | glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity |
| A | 0005634 | cellular_component | nucleus |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005739 | cellular_component | mitochondrion |
| A | 0005811 | cellular_component | lipid droplet |
| A | 0005829 | cellular_component | cytosol |
| A | 0005886 | cellular_component | plasma membrane |
| A | 0006006 | biological_process | glucose metabolic process |
| A | 0006094 | biological_process | gluconeogenesis |
| A | 0006096 | biological_process | glycolytic process |
| A | 0006915 | biological_process | apoptotic process |
| A | 0009277 | cellular_component | fungal-type cell wall |
| A | 0015886 | biological_process | heme transport |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0016620 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor |
| A | 0020037 | molecular_function | heme binding |
| A | 0050661 | molecular_function | NADP binding |
| A | 0051287 | molecular_function | NAD binding |
| A | 0072593 | biological_process | reactive oxygen species metabolic process |
| A | 1904408 | molecular_function | melatonin binding |
| B | 0003723 | molecular_function | RNA binding |
| B | 0003729 | molecular_function | mRNA binding |
| B | 0004365 | molecular_function | glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity |
| B | 0005634 | cellular_component | nucleus |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005739 | cellular_component | mitochondrion |
| B | 0005811 | cellular_component | lipid droplet |
| B | 0005829 | cellular_component | cytosol |
| B | 0005886 | cellular_component | plasma membrane |
| B | 0006006 | biological_process | glucose metabolic process |
| B | 0006094 | biological_process | gluconeogenesis |
| B | 0006096 | biological_process | glycolytic process |
| B | 0006915 | biological_process | apoptotic process |
| B | 0009277 | cellular_component | fungal-type cell wall |
| B | 0015886 | biological_process | heme transport |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0016620 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor |
| B | 0020037 | molecular_function | heme binding |
| B | 0050661 | molecular_function | NADP binding |
| B | 0051287 | molecular_function | NAD binding |
| B | 0072593 | biological_process | reactive oxygen species metabolic process |
| B | 1904408 | molecular_function | melatonin binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 24 |
| Details | BINDING SITE FOR RESIDUE NAD A 333 |
| Chain | Residue |
| A | ASN7 |
| A | THR97 |
| A | GLY98 |
| A | THR120 |
| A | ALA121 |
| A | CYS150 |
| A | ALA181 |
| A | ASN314 |
| A | TYR318 |
| A | HOH360 |
| A | HOH377 |
| A | GLY8 |
| A | HOH409 |
| A | HOH447 |
| A | HOH566 |
| B | HOH380 |
| B | HOH456 |
| A | GLY10 |
| A | ARG11 |
| A | ILE12 |
| A | ASP33 |
| A | PRO34 |
| A | ARG78 |
| A | SER96 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MRY A 334 |
| Chain | Residue |
| A | ALA42 |
| A | TYR43 |
| A | VAL58 |
| A | HIS60 |
| A | HOH385 |
| B | ASP277 |
| site_id | AC3 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE NAD B 333 |
| Chain | Residue |
| A | HOH397 |
| B | ASN7 |
| B | GLY8 |
| B | GLY10 |
| B | ARG11 |
| B | ILE12 |
| B | ASP33 |
| B | PRO34 |
| B | SER96 |
| B | THR97 |
| B | GLY98 |
| B | THR120 |
| B | ALA121 |
| B | CYS150 |
| B | ALA181 |
| B | ASN314 |
| B | TYR318 |
| B | HOH400 |
| B | HOH411 |
| B | HOH534 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MRY B 334 |
| Chain | Residue |
| A | ASP277 |
| B | ALA42 |
| B | TYR43 |
| B | VAL58 |
| B | HOH379 |
| B | HOH434 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA B 504 |
| Chain | Residue |
| B | ALA20 |
| B | LEU21 |
| B | ARG23 |
| B | VAL26 |
| B | HOH519 |
Functional Information from PROSITE/UniProt
| site_id | PS00071 |
| Number of Residues | 8 |
| Details | GAPDH Glyceraldehyde 3-phosphate dehydrogenase active site. ASCTTNcL |
| Chain | Residue | Details |
| A | ALA148-LEU155 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Nucleophile","evidences":[{"source":"PROSITE-ProRule","id":"PRU10009","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 12 |
| Details | Binding site: {"evidences":[{"source":"PDB","id":"3PYM","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 10 |
| Details | Binding site: {"evidences":[{"source":"UniProtKB","id":"P22513","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | Site: {"description":"Activates thiol group during catalysis","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"Cysteine persulfide","evidences":[{"source":"PubMed","id":"36102610","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 4 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"22106047","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 6 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in URM1)","evidences":[{"source":"PubMed","id":"36102610","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
