5DDI
Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from pig muscle - holo enzyme - at 2.40 Angstrom resolution
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| P | 0000226 | biological_process | microtubule cytoskeleton organization |
| P | 0004365 | molecular_function | glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity |
| P | 0005634 | cellular_component | nucleus |
| P | 0005737 | cellular_component | cytoplasm |
| P | 0005829 | cellular_component | cytosol |
| P | 0005856 | cellular_component | cytoskeleton |
| P | 0006006 | biological_process | glucose metabolic process |
| P | 0006096 | biological_process | glycolytic process |
| P | 0006417 | biological_process | regulation of translation |
| P | 0006915 | biological_process | apoptotic process |
| P | 0008017 | molecular_function | microtubule binding |
| P | 0015630 | cellular_component | microtubule cytoskeleton |
| P | 0016491 | molecular_function | oxidoreductase activity |
| P | 0016620 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor |
| P | 0016740 | molecular_function | transferase activity |
| P | 0032481 | biological_process | positive regulation of type I interferon production |
| P | 0035605 | molecular_function | peptidyl-cysteine S-nitrosylase activity |
| P | 0035606 | biological_process | peptidyl-cysteine S-trans-nitrosylation |
| P | 0043123 | biological_process | positive regulation of canonical NF-kappaB signal transduction |
| P | 0045087 | biological_process | innate immune response |
| P | 0050661 | molecular_function | NADP binding |
| P | 0050821 | biological_process | protein stabilization |
| P | 0051287 | molecular_function | NAD binding |
| P | 0051402 | biological_process | neuron apoptotic process |
| P | 0097452 | cellular_component | GAIT complex |
| R | 0000226 | biological_process | microtubule cytoskeleton organization |
| R | 0004365 | molecular_function | glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity |
| R | 0005634 | cellular_component | nucleus |
| R | 0005737 | cellular_component | cytoplasm |
| R | 0005829 | cellular_component | cytosol |
| R | 0005856 | cellular_component | cytoskeleton |
| R | 0006006 | biological_process | glucose metabolic process |
| R | 0006096 | biological_process | glycolytic process |
| R | 0006417 | biological_process | regulation of translation |
| R | 0006915 | biological_process | apoptotic process |
| R | 0008017 | molecular_function | microtubule binding |
| R | 0015630 | cellular_component | microtubule cytoskeleton |
| R | 0016491 | molecular_function | oxidoreductase activity |
| R | 0016620 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor |
| R | 0016740 | molecular_function | transferase activity |
| R | 0032481 | biological_process | positive regulation of type I interferon production |
| R | 0035605 | molecular_function | peptidyl-cysteine S-nitrosylase activity |
| R | 0035606 | biological_process | peptidyl-cysteine S-trans-nitrosylation |
| R | 0043123 | biological_process | positive regulation of canonical NF-kappaB signal transduction |
| R | 0045087 | biological_process | innate immune response |
| R | 0050661 | molecular_function | NADP binding |
| R | 0050821 | biological_process | protein stabilization |
| R | 0051287 | molecular_function | NAD binding |
| R | 0051402 | biological_process | neuron apoptotic process |
| R | 0097452 | cellular_component | GAIT complex |
| S | 0000226 | biological_process | microtubule cytoskeleton organization |
| S | 0004365 | molecular_function | glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity |
| S | 0005634 | cellular_component | nucleus |
| S | 0005737 | cellular_component | cytoplasm |
| S | 0005829 | cellular_component | cytosol |
| S | 0005856 | cellular_component | cytoskeleton |
| S | 0006006 | biological_process | glucose metabolic process |
| S | 0006096 | biological_process | glycolytic process |
| S | 0006417 | biological_process | regulation of translation |
| S | 0006915 | biological_process | apoptotic process |
| S | 0008017 | molecular_function | microtubule binding |
| S | 0015630 | cellular_component | microtubule cytoskeleton |
| S | 0016491 | molecular_function | oxidoreductase activity |
| S | 0016620 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor |
| S | 0016740 | molecular_function | transferase activity |
| S | 0032481 | biological_process | positive regulation of type I interferon production |
| S | 0035605 | molecular_function | peptidyl-cysteine S-nitrosylase activity |
| S | 0035606 | biological_process | peptidyl-cysteine S-trans-nitrosylation |
| S | 0043123 | biological_process | positive regulation of canonical NF-kappaB signal transduction |
| S | 0045087 | biological_process | innate immune response |
| S | 0050661 | molecular_function | NADP binding |
| S | 0050821 | biological_process | protein stabilization |
| S | 0051287 | molecular_function | NAD binding |
| S | 0051402 | biological_process | neuron apoptotic process |
| S | 0097452 | cellular_component | GAIT complex |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 P 501 |
| Chain | Residue |
| P | SER148 |
| P | THR208 |
| P | GLY209 |
| P | ALA210 |
| P | HOH620 |
| P | HOH640 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 P 502 |
| Chain | Residue |
| P | THR179 |
| P | THR181 |
| P | ARG231 |
| site_id | AC3 |
| Number of Residues | 16 |
| Details | binding site for residue NAD P 503 |
| Chain | Residue |
| P | PHE8 |
| P | GLY9 |
| P | ARG10 |
| P | ILE11 |
| P | ASP32 |
| P | PRO33 |
| P | PHE34 |
| P | ARG77 |
| P | THR96 |
| P | GLY97 |
| P | SER119 |
| P | ASN313 |
| P | HOH605 |
| P | HOH613 |
| P | HOH657 |
| R | HOH610 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 R 501 |
| Chain | Residue |
| R | SER148 |
| R | THR208 |
| R | GLY209 |
| R | ALA210 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 R 502 |
| Chain | Residue |
| R | THR179 |
| R | THR181 |
| R | ARG231 |
| R | NAD503 |
| site_id | AC6 |
| Number of Residues | 13 |
| Details | binding site for residue NAD R 503 |
| Chain | Residue |
| R | GLY9 |
| R | ARG10 |
| R | ILE11 |
| R | ASN31 |
| R | ASP32 |
| R | PRO33 |
| R | ARG77 |
| R | SER95 |
| R | THR96 |
| R | GLY97 |
| R | SER119 |
| R | ASN313 |
| R | SO4502 |
| site_id | AC7 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 S 501 |
| Chain | Residue |
| S | THR208 |
| S | GLY209 |
| S | ALA210 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 S 502 |
| Chain | Residue |
| S | THR179 |
| S | THR181 |
| S | ARG231 |
| S | NAD503 |
| S | HOH615 |
| S | HOH624 |
| site_id | AC9 |
| Number of Residues | 18 |
| Details | binding site for residue NAD S 503 |
| Chain | Residue |
| S | PHE8 |
| S | GLY9 |
| S | ARG10 |
| S | ILE11 |
| S | ASP32 |
| S | PRO33 |
| S | PHE34 |
| S | ARG77 |
| S | THR96 |
| S | GLY97 |
| S | SER119 |
| S | ALA120 |
| S | ASN313 |
| S | SO4502 |
| S | HOH620 |
| S | HOH624 |
| S | HOH625 |
| S | HOH666 |
Functional Information from PROSITE/UniProt
| site_id | PS00071 |
| Number of Residues | 8 |
| Details | GAPDH Glyceraldehyde 3-phosphate dehydrogenase active site. ASCTTNcL |
| Chain | Residue | Details |
| P | ALA147-LEU154 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 3 |
| Details | ACT_SITE: Nucleophile => ECO:0000255|PROSITE-ProRule:PRU10009 |
| Chain | Residue | Details |
| P | CYS149 | |
| R | CYS149 | |
| S | CYS149 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 15 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:P04406 |
| Chain | Residue | Details |
| P | ARG10 | |
| R | ASN313 | |
| S | ARG10 | |
| S | ASP32 | |
| S | ARG77 | |
| S | SER119 | |
| S | ASN313 | |
| P | ASP32 | |
| P | ARG77 | |
| P | SER119 | |
| P | ASN313 | |
| R | ARG10 | |
| R | ASP32 | |
| R | ARG77 | |
| R | SER119 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:P22513 |
| Chain | Residue | Details |
| P | SER148 | |
| S | THR179 | |
| S | THR208 | |
| S | ARG231 | |
| P | THR179 | |
| P | THR208 | |
| P | ARG231 | |
| R | SER148 | |
| R | THR179 | |
| R | THR208 | |
| R | ARG231 | |
| S | SER148 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 3 |
| Details | SITE: Activates thiol group during catalysis => ECO:0000250|UniProtKB:P04406 |
| Chain | Residue | Details |
| P | HIS176 | |
| R | HIS176 | |
| S | HIS176 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 15 |
| Details | MOD_RES: N6,N6-dimethyllysine => ECO:0000250|UniProtKB:P04406 |
| Chain | Residue | Details |
| P | LYS2 | |
| R | LYS331 | |
| S | LYS2 | |
| S | LYS63 | |
| S | GLN257 | |
| S | LYS260 | |
| S | LYS331 | |
| P | LYS63 | |
| P | GLN257 | |
| P | LYS260 | |
| P | LYS331 | |
| R | LYS2 | |
| R | LYS63 | |
| R | GLN257 | |
| R | LYS260 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 21 |
| Details | MOD_RES: Deamidated asparagine => ECO:0000250|UniProtKB:P04406 |
| Chain | Residue | Details |
| P | ASN6 | |
| R | ASN67 | |
| R | ASN146 | |
| R | ASN152 | |
| R | ASN222 | |
| R | ASN313 | |
| S | ASN6 | |
| S | ASN61 | |
| S | ASN67 | |
| S | ASN146 | |
| S | ASN152 | |
| P | ASN61 | |
| S | ASN222 | |
| S | ASN313 | |
| P | ASN67 | |
| P | ASN146 | |
| P | ASN152 | |
| P | ASN222 | |
| P | ASN313 | |
| R | ASN6 | |
| R | ASN61 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 3 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P04406 |
| Chain | Residue | Details |
| P | TYR39 | |
| R | TYR39 | |
| S | TYR39 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 9 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P04406 |
| Chain | Residue | Details |
| P | LYS58 | |
| P | LYS216 | |
| P | LYS251 | |
| R | LYS58 | |
| R | LYS216 | |
| R | LYS251 | |
| S | LYS58 | |
| S | LYS216 | |
| S | LYS251 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 24 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:P04406 |
| Chain | Residue | Details |
| P | THR72 | |
| R | THR150 | |
| R | THR174 | |
| R | THR179 | |
| R | THR181 | |
| R | THR208 | |
| R | THR226 | |
| R | THR234 | |
| S | THR72 | |
| S | THR150 | |
| S | THR174 | |
| P | THR150 | |
| S | THR179 | |
| S | THR181 | |
| S | THR208 | |
| S | THR226 | |
| S | THR234 | |
| P | THR174 | |
| P | THR179 | |
| P | THR181 | |
| P | THR208 | |
| P | THR226 | |
| P | THR234 | |
| R | THR72 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 18 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P04406 |
| Chain | Residue | Details |
| P | SER119 | |
| R | SER238 | |
| R | SER309 | |
| R | SER330 | |
| S | SER119 | |
| S | SER145 | |
| S | SER148 | |
| S | SER238 | |
| S | SER309 | |
| S | SER330 | |
| P | SER145 | |
| P | SER148 | |
| P | SER238 | |
| P | SER309 | |
| P | SER330 | |
| R | SER119 | |
| R | SER145 | |
| R | SER148 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 3 |
| Details | MOD_RES: S-nitrosocysteine; in reversibly inhibited form => ECO:0000250|UniProtKB:P04797 |
| Chain | Residue | Details |
| P | CYS149 | |
| R | CYS149 | |
| S | CYS149 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 6 |
| Details | MOD_RES: N6-malonyllysine; alternate => ECO:0000250|UniProtKB:P04406 |
| Chain | Residue | Details |
| P | LYS191 | |
| P | LYS212 | |
| R | LYS191 | |
| R | LYS212 | |
| S | LYS191 | |
| S | LYS212 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 3 |
| Details | MOD_RES: N6-acetyllysine; alternate => ECO:0000250|UniProtKB:P04406 |
| Chain | Residue | Details |
| P | LYS224 | |
| R | LYS224 | |
| S | LYS224 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 3 |
| Details | MOD_RES: S-nitrosocysteine => ECO:0000250|UniProtKB:P04406 |
| Chain | Residue | Details |
| P | CYS244 | |
| R | CYS244 | |
| S | CYS244 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 6 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0000250|UniProtKB:P04406 |
| Chain | Residue | Details |
| P | LYS183 | |
| R | LYS183 | |
| S | LYS183 |
