3GPD
TWINNING IN CRYSTALS OF HUMAN SKELETAL MUSCLE D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| G | 0000226 | biological_process | microtubule cytoskeleton organization |
| G | 0001819 | biological_process | positive regulation of cytokine production |
| G | 0004365 | molecular_function | glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity |
| G | 0005515 | molecular_function | protein binding |
| G | 0005634 | cellular_component | nucleus |
| G | 0005737 | cellular_component | cytoplasm |
| G | 0005811 | cellular_component | lipid droplet |
| G | 0005829 | cellular_component | cytosol |
| G | 0005856 | cellular_component | cytoskeleton |
| G | 0005886 | cellular_component | plasma membrane |
| G | 0006006 | biological_process | glucose metabolic process |
| G | 0006096 | biological_process | glycolytic process |
| G | 0006417 | biological_process | regulation of translation |
| G | 0006915 | biological_process | apoptotic process |
| G | 0008017 | molecular_function | microtubule binding |
| G | 0010951 | biological_process | negative regulation of endopeptidase activity |
| G | 0015630 | cellular_component | microtubule cytoskeleton |
| G | 0016020 | cellular_component | membrane |
| G | 0016241 | biological_process | regulation of macroautophagy |
| G | 0016491 | molecular_function | oxidoreductase activity |
| G | 0016620 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor |
| G | 0016740 | molecular_function | transferase activity |
| G | 0017148 | biological_process | negative regulation of translation |
| G | 0019828 | molecular_function | aspartic-type endopeptidase inhibitor activity |
| G | 0031640 | biological_process | killing of cells of another organism |
| G | 0031965 | cellular_component | nuclear membrane |
| G | 0031982 | cellular_component | vesicle |
| G | 0032481 | biological_process | positive regulation of type I interferon production |
| G | 0035605 | molecular_function | peptidyl-cysteine S-nitrosylase activity |
| G | 0035606 | biological_process | peptidyl-cysteine S-trans-nitrosylation |
| G | 0042802 | molecular_function | identical protein binding |
| G | 0043123 | biological_process | positive regulation of canonical NF-kappaB signal transduction |
| G | 0043231 | cellular_component | intracellular membrane-bounded organelle |
| G | 0045087 | biological_process | innate immune response |
| G | 0048471 | cellular_component | perinuclear region of cytoplasm |
| G | 0050661 | molecular_function | NADP binding |
| G | 0050821 | biological_process | protein stabilization |
| G | 0050832 | biological_process | defense response to fungus |
| G | 0051287 | molecular_function | NAD binding |
| G | 0051402 | biological_process | neuron apoptotic process |
| G | 0051873 | biological_process | killing by host of symbiont cells |
| G | 0061844 | biological_process | antimicrobial humoral immune response mediated by antimicrobial peptide |
| G | 0070062 | cellular_component | extracellular exosome |
| G | 0071346 | biological_process | cellular response to type II interferon |
| G | 0097452 | cellular_component | GAIT complex |
| G | 0097718 | molecular_function | disordered domain specific binding |
| G | 1990904 | cellular_component | ribonucleoprotein complex |
| R | 0000226 | biological_process | microtubule cytoskeleton organization |
| R | 0001819 | biological_process | positive regulation of cytokine production |
| R | 0004365 | molecular_function | glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity |
| R | 0005515 | molecular_function | protein binding |
| R | 0005634 | cellular_component | nucleus |
| R | 0005737 | cellular_component | cytoplasm |
| R | 0005811 | cellular_component | lipid droplet |
| R | 0005829 | cellular_component | cytosol |
| R | 0005856 | cellular_component | cytoskeleton |
| R | 0005886 | cellular_component | plasma membrane |
| 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 | 0010951 | biological_process | negative regulation of endopeptidase activity |
| R | 0015630 | cellular_component | microtubule cytoskeleton |
| R | 0016020 | cellular_component | membrane |
| R | 0016241 | biological_process | regulation of macroautophagy |
| 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 | 0017148 | biological_process | negative regulation of translation |
| R | 0019828 | molecular_function | aspartic-type endopeptidase inhibitor activity |
| R | 0031640 | biological_process | killing of cells of another organism |
| R | 0031965 | cellular_component | nuclear membrane |
| R | 0031982 | cellular_component | vesicle |
| 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 | 0042802 | molecular_function | identical protein binding |
| R | 0043123 | biological_process | positive regulation of canonical NF-kappaB signal transduction |
| R | 0043231 | cellular_component | intracellular membrane-bounded organelle |
| R | 0045087 | biological_process | innate immune response |
| R | 0048471 | cellular_component | perinuclear region of cytoplasm |
| R | 0050661 | molecular_function | NADP binding |
| R | 0050821 | biological_process | protein stabilization |
| R | 0050832 | biological_process | defense response to fungus |
| R | 0051287 | molecular_function | NAD binding |
| R | 0051402 | biological_process | neuron apoptotic process |
| R | 0051873 | biological_process | killing by host of symbiont cells |
| R | 0061844 | biological_process | antimicrobial humoral immune response mediated by antimicrobial peptide |
| R | 0070062 | cellular_component | extracellular exosome |
| R | 0071346 | biological_process | cellular response to type II interferon |
| R | 0097452 | cellular_component | GAIT complex |
| R | 0097718 | molecular_function | disordered domain specific binding |
| R | 1990904 | cellular_component | ribonucleoprotein complex |
Functional Information from PDB Data
| site_id | ABR |
| Number of Residues | 8 |
| Details | RESIDUES INTERACTING WITH THE ADENINE BASE OF THE NAD COFACTOR IN THE RED SUBUNIT |
| Chain | Residue |
| R | ASP8 |
| R | GLY9 |
| R | ASN33 |
| R | ASP34 |
| R | PRO35 |
| R | GLU78 |
| R | ARG79 |
| R | ASP80 |
| site_id | AC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 R 338 |
| Chain | Residue |
| R | THR181 |
| R | THR183 |
| R | NAD336 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 R 340 |
| Chain | Residue |
| R | SER150 |
| R | CYS151 |
| R | THR210 |
| R | GLY211 |
| site_id | AC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 G 338 |
| Chain | Residue |
| G | THR181 |
| G | THR183 |
| G | NAD336 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 G 340 |
| Chain | Residue |
| G | SER150 |
| G | CYS151 |
| G | THR152 |
| G | THR210 |
| G | GLY211 |
| site_id | AC5 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE NAD R 336 |
| Chain | Residue |
| R | GLY9 |
| R | GLY11 |
| R | ARG12 |
| R | ILE13 |
| R | ASN33 |
| R | ASP34 |
| R | PRO35 |
| R | PHE36 |
| R | GLU78 |
| R | ASP80 |
| R | SER97 |
| R | THR98 |
| R | SER121 |
| R | ALA122 |
| R | CYS151 |
| R | ILE180 |
| R | ALA182 |
| R | ASN315 |
| R | GLU316 |
| R | SO4338 |
| site_id | AC6 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE NAD G 336 |
| Chain | Residue |
| G | GLY9 |
| G | GLY11 |
| G | ARG12 |
| G | ILE13 |
| G | PRO35 |
| G | ARG79 |
| G | SER97 |
| G | THR98 |
| G | GLY99 |
| G | PHE101 |
| G | SER121 |
| G | ALA122 |
| G | CYS151 |
| G | ALA182 |
| G | ASN315 |
| G | SO4338 |
| site_id | APR |
| Number of Residues | 2 |
| Details | RESIDUES INTERACTING WITH THE PHOSPHATE OF THE ADENOSINE NUCLEOTIDE OF THE NAD COFACTOR IN THE RED SUBUNIT |
| Chain | Residue |
| R | GLY11 |
| R | ARG12 |
| site_id | ARR |
| Number of Residues | 3 |
| Details | RESIDUES INTERACTING WITH THE ADENOSINE RIBOSE OF THE NAD COFACTOR IN THE RED SUBUNIT |
| Chain | Residue |
| R | SER97 |
| R | THR98 |
| R | PHE36 |
| site_id | IPR |
| Number of Residues | 4 |
| Details | RESIDUES INTERACTING WITH THE SUBSTRATE AND THE INORGANIC PHOSPHATE GROUPS RESPECTIVELY OF THE RED SUBUNIT |
| Chain | Residue |
| R | THR181 |
| R | ALA182 |
| R | THR183 |
| R | ARG233 |
| site_id | NBR |
| Number of Residues | 4 |
| Details | RESIDUES INTERACTING WITH THE NICOTINAMIDE BASE OF THE NAD COFACTOR IN THE RED SUBUNIT |
| Chain | Residue |
| R | CYS151 |
| R | ILE180 |
| R | ASN315 |
| R | GLU316 |
| site_id | NPR |
| Number of Residues | 2 |
| Details | RESIDUES INTERACTING WITH THE PHOSPHATE OF THE NICOTINAMIDE NUCLEOTIDE OF THE NAD COFACTOR IN THE RED SUBUNIT |
| Chain | Residue |
| R | ARG12 |
| R | ILE13 |
| site_id | NRR |
| Number of Residues | 3 |
| Details | RESIDUES INTERACTING WITH THE RIBOSE OF THE NICOTINAMIDE NUCLEOTIDE OF THE NAD COFACTOR IN THE RED SUBUNIT |
| Chain | Residue |
| R | ILE13 |
| R | SER121 |
| R | ALA122 |
| site_id | SPR |
| Number of Residues | 4 |
| Details | RESIDUES INTERACTING WITH THE SUBSTRATE AND THE INORGANIC PHOSPHATE GROUPS RESPECTIVELY OF THE RED SUBUNIT |
| Chain | Residue |
| R | SER150 |
| R | CYS151 |
| R | THR152 |
| R | THR210 |
Functional Information from PROSITE/UniProt
| site_id | PS00071 |
| Number of Residues | 8 |
| Details | GAPDH Glyceraldehyde 3-phosphate dehydrogenase active site. ASCTTNcL |
| Chain | Residue | Details |
| R | ALA149-LEU156 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | ACT_SITE: Nucleophile => ECO:0000269|PubMed:25086035 |
| Chain | Residue | Details |
| R | THR152 | |
| G | THR152 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 10 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:16239728, ECO:0000269|PubMed:16510976 |
| Chain | Residue | Details |
| R | ILE13 | |
| G | GLU316 | |
| R | PRO35 | |
| R | ASP80 | |
| R | ALA122 | |
| R | GLU316 | |
| G | ILE13 | |
| G | PRO35 | |
| G | ASP80 | |
| G | ALA122 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:P22513 |
| Chain | Residue | Details |
| R | CYS151 | |
| R | ALA182 | |
| R | GLY211 | |
| R | VAL234 | |
| G | CYS151 | |
| G | ALA182 | |
| G | GLY211 | |
| G | VAL234 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | SITE: Activates thiol group during catalysis => ECO:0000305|PubMed:16239728, ECO:0000305|PubMed:16510976 |
| Chain | Residue | Details |
| R | ALA179 | |
| G | ALA179 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 10 |
| Details | MOD_RES: N6,N6-dimethyllysine => ECO:0000269|PubMed:18183946 |
| Chain | Residue | Details |
| R | VAL5 | |
| G | GLU334 | |
| R | LEU66 | |
| R | VAL260 | |
| R | GLU263 | |
| R | GLU334 | |
| G | VAL5 | |
| G | LEU66 | |
| G | VAL260 | |
| G | GLU263 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 14 |
| Details | MOD_RES: Deamidated asparagine => ECO:0000269|PubMed:18183946 |
| Chain | Residue | Details |
| R | GLY9 | |
| G | GLY70 | |
| G | ALA149 | |
| G | CYS155 | |
| G | GLY225 | |
| G | GLU316 | |
| R | GLY64 | |
| R | GLY70 | |
| R | ALA149 | |
| R | CYS155 | |
| R | GLY225 | |
| R | GLU316 | |
| G | GLY9 | |
| G | GLY64 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphotyrosine => ECO:0007744|PubMed:15592455 |
| Chain | Residue | Details |
| R | MET42 | |
| G | MET42 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | MOD_RES: Methionine sulfoxide; in vitro => ECO:0000305|PubMed:25086035 |
| Chain | Residue | Details |
| R | PHE46 | |
| G | PHE46 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 6 |
| Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
| Chain | Residue | Details |
| R | ALA61 | |
| R | VAL219 | |
| R | TYR254 | |
| G | ALA61 | |
| G | VAL219 | |
| G | TYR254 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0000269|PubMed:18183946, ECO:0007744|PubMed:20068231 |
| Chain | Residue | Details |
| R | ILE75 | |
| G | ILE75 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| R | ASN83 | |
| G | ASN83 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:18183946 |
| Chain | Residue | Details |
| R | ALA122 | |
| R | ASN148 | |
| G | ALA122 | |
| G | ASN148 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| R | CYS151 | |
| G | CYS151 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 2 |
| Details | MOD_RES: S-nitrosocysteine; in reversibly inhibited form => ECO:0000250|UniProtKB:P04797 |
| Chain | Residue | Details |
| R | THR152 | |
| G | THR152 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| R | THR153 | |
| G | THR153 |
| site_id | SWS_FT_FI16 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| R | VAL177 | |
| R | ALA182 | |
| G | VAL177 | |
| G | ALA182 |
| site_id | SWS_FT_FI17 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| R | GLN184 | |
| G | GLN184 |
| site_id | SWS_FT_FI18 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-malonyllysine; alternate => ECO:0000269|PubMed:21908771 |
| Chain | Residue | Details |
| R | LEU194 | |
| R | ALA215 | |
| G | LEU194 | |
| G | ALA215 |
| site_id | SWS_FT_FI19 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:19690332 |
| Chain | Residue | Details |
| R | GLY211 | |
| G | GLY211 |
| site_id | SWS_FT_FI20 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-acetyllysine; alternate => ECO:0007744|PubMed:19608861 |
| Chain | Residue | Details |
| R | LEU227 | |
| G | LEU227 |
| site_id | SWS_FT_FI21 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0000269|PubMed:18183946, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| R | GLY229 | |
| G | GLY229 |
| site_id | SWS_FT_FI22 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0000269|PubMed:18183946 |
| Chain | Residue | Details |
| R | ALA237 | |
| G | ALA237 |
| site_id | SWS_FT_FI23 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| R | VAL241 | |
| G | VAL241 |
| site_id | SWS_FT_FI24 |
| Number of Residues | 2 |
| Details | MOD_RES: S-nitrosocysteine => ECO:0000269|PubMed:22771119, ECO:0000269|PubMed:25417112 |
| Chain | Residue | Details |
| R | ARG247 | |
| G | ARG247 |
| site_id | SWS_FT_FI25 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:18183946, ECO:0007744|PubMed:19690332 |
| Chain | Residue | Details |
| R | TRP312 | |
| G | TRP312 |
| site_id | SWS_FT_FI26 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| R | LYS333 | |
| G | LYS333 |
| site_id | SWS_FT_FI27 |
| Number of Residues | 4 |
| Details | CARBOHYD: (Microbial infection) N-beta-linked (GlcNAc) arginine => ECO:0000269|PubMed:28522607 |
| Chain | Residue | Details |
| R | GLY197 | |
| R | GLY200 | |
| G | GLY197 | |
| G | GLY200 |
| site_id | SWS_FT_FI28 |
| Number of Residues | 4 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| R | THR186 | |
| G | THR186 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1szj |
| Chain | Residue | Details |
| R | CYS151 | |
| R | HIS178 |
| site_id | CSA2 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1szj |
| Chain | Residue | Details |
| G | CYS151 | |
| G | HIS178 |
