2GCG
Ternary Crystal Structure of Human Glyoxylate Reductase/Hydroxypyruvate Reductase
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0005515 | molecular_function | protein binding |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005782 | cellular_component | peroxisomal matrix |
| A | 0005829 | cellular_component | cytosol |
| A | 0008465 | molecular_function | hydroxypyruvate reductase (NADH) activity |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| A | 0016618 | molecular_function | hydroxypyruvate reductase [NAD(P)H] activity |
| A | 0019752 | biological_process | carboxylic acid metabolic process |
| A | 0030267 | molecular_function | glyoxylate reductase (NADPH) activity |
| A | 0031406 | molecular_function | carboxylic acid binding |
| A | 0042803 | molecular_function | protein homodimerization activity |
| A | 0043648 | biological_process | dicarboxylic acid metabolic process |
| A | 0046487 | biological_process | glyoxylate metabolic process |
| A | 0050661 | molecular_function | NADP binding |
| A | 0051287 | molecular_function | NAD binding |
| A | 0070062 | cellular_component | extracellular exosome |
| A | 0070402 | molecular_function | NADPH binding |
| A | 1902494 | cellular_component | catalytic complex |
| B | 0005515 | molecular_function | protein binding |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005782 | cellular_component | peroxisomal matrix |
| B | 0005829 | cellular_component | cytosol |
| B | 0008465 | molecular_function | hydroxypyruvate reductase (NADH) activity |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| B | 0016618 | molecular_function | hydroxypyruvate reductase [NAD(P)H] activity |
| B | 0019752 | biological_process | carboxylic acid metabolic process |
| B | 0030267 | molecular_function | glyoxylate reductase (NADPH) activity |
| B | 0031406 | molecular_function | carboxylic acid binding |
| B | 0042803 | molecular_function | protein homodimerization activity |
| B | 0043648 | biological_process | dicarboxylic acid metabolic process |
| B | 0046487 | biological_process | glyoxylate metabolic process |
| B | 0050661 | molecular_function | NADP binding |
| B | 0051287 | molecular_function | NAD binding |
| B | 0070062 | cellular_component | extracellular exosome |
| B | 0070402 | molecular_function | NADPH binding |
| B | 1902494 | cellular_component | catalytic complex |
| C | 0005515 | molecular_function | protein binding |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005782 | cellular_component | peroxisomal matrix |
| C | 0005829 | cellular_component | cytosol |
| C | 0008465 | molecular_function | hydroxypyruvate reductase (NADH) activity |
| C | 0016491 | molecular_function | oxidoreductase activity |
| C | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| C | 0016618 | molecular_function | hydroxypyruvate reductase [NAD(P)H] activity |
| C | 0019752 | biological_process | carboxylic acid metabolic process |
| C | 0030267 | molecular_function | glyoxylate reductase (NADPH) activity |
| C | 0031406 | molecular_function | carboxylic acid binding |
| C | 0042803 | molecular_function | protein homodimerization activity |
| C | 0043648 | biological_process | dicarboxylic acid metabolic process |
| C | 0046487 | biological_process | glyoxylate metabolic process |
| C | 0050661 | molecular_function | NADP binding |
| C | 0051287 | molecular_function | NAD binding |
| C | 0070062 | cellular_component | extracellular exosome |
| C | 0070402 | molecular_function | NADPH binding |
| C | 1902494 | cellular_component | catalytic complex |
| D | 0005515 | molecular_function | protein binding |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0005782 | cellular_component | peroxisomal matrix |
| D | 0005829 | cellular_component | cytosol |
| D | 0008465 | molecular_function | hydroxypyruvate reductase (NADH) activity |
| D | 0016491 | molecular_function | oxidoreductase activity |
| D | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| D | 0016618 | molecular_function | hydroxypyruvate reductase [NAD(P)H] activity |
| D | 0019752 | biological_process | carboxylic acid metabolic process |
| D | 0030267 | molecular_function | glyoxylate reductase (NADPH) activity |
| D | 0031406 | molecular_function | carboxylic acid binding |
| D | 0042803 | molecular_function | protein homodimerization activity |
| D | 0043648 | biological_process | dicarboxylic acid metabolic process |
| D | 0046487 | biological_process | glyoxylate metabolic process |
| D | 0050661 | molecular_function | NADP binding |
| D | 0051287 | molecular_function | NAD binding |
| D | 0070062 | cellular_component | extracellular exosome |
| D | 0070402 | molecular_function | NADPH binding |
| D | 1902494 | cellular_component | catalytic complex |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 C 1001 |
| Chain | Residue |
| C | GLY150 |
| C | THR152 |
| C | GLN153 |
| C | SER154 |
| D | ARG300 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 D 1002 |
| Chain | Residue |
| C | ASP37 |
| D | LEU144 |
| D | SO41003 |
| site_id | AC3 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SO4 D 1003 |
| Chain | Residue |
| D | LEU144 |
| D | TRP145 |
| D | LEU146 |
| D | SO41002 |
| D | HOH2033 |
| D | HOH2100 |
| D | HOH2120 |
| D | ARG125 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 D 1004 |
| Chain | Residue |
| C | ARG300 |
| D | GLY150 |
| D | THR152 |
| D | GLN153 |
| D | SER154 |
| D | HOH2067 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1005 |
| Chain | Residue |
| A | ARG300 |
| B | GLY150 |
| B | THR152 |
| B | GLN153 |
| B | SER154 |
| site_id | AC6 |
| Number of Residues | 28 |
| Details | BINDING SITE FOR RESIDUE NDP A 2001 |
| Chain | Residue |
| A | VAL83 |
| A | THR111 |
| A | ILE159 |
| A | GLY160 |
| A | LEU161 |
| A | GLY162 |
| A | ARG163 |
| A | ILE164 |
| A | GLY184 |
| A | ARG185 |
| A | GLN186 |
| A | ARG188 |
| A | CYS216 |
| A | SER217 |
| A | THR222 |
| A | ILE243 |
| A | SER244 |
| A | ARG245 |
| A | ASP269 |
| A | HIS293 |
| A | GLY295 |
| A | SER296 |
| A | DGY3001 |
| A | HOH3003 |
| A | HOH3012 |
| A | HOH3021 |
| A | HOH3030 |
| A | HOH3169 |
| site_id | AC7 |
| Number of Residues | 31 |
| Details | BINDING SITE FOR RESIDUE NDP B 2002 |
| Chain | Residue |
| B | VAL83 |
| B | THR111 |
| B | ILE159 |
| B | GLY160 |
| B | LEU161 |
| B | GLY162 |
| B | ARG163 |
| B | ILE164 |
| B | THR183 |
| B | GLY184 |
| B | ARG185 |
| B | GLN186 |
| B | ARG188 |
| B | ALA215 |
| B | CYS216 |
| B | SER217 |
| B | THR222 |
| B | ILE243 |
| B | SER244 |
| B | ARG245 |
| B | ASP269 |
| B | HIS293 |
| B | GLY295 |
| B | SER296 |
| B | HOH2008 |
| B | HOH2013 |
| B | HOH2023 |
| B | HOH2030 |
| B | HOH2035 |
| B | HOH2043 |
| B | HOH2045 |
| site_id | AC8 |
| Number of Residues | 29 |
| Details | BINDING SITE FOR RESIDUE NDP C 2003 |
| Chain | Residue |
| C | SER217 |
| C | THR222 |
| C | ILE243 |
| C | SER244 |
| C | ARG245 |
| C | ASP269 |
| C | HIS293 |
| C | GLY295 |
| C | SER296 |
| C | DGY3002 |
| C | HOH3008 |
| C | HOH3012 |
| C | HOH3020 |
| C | HOH3022 |
| C | HOH3040 |
| C | HOH3078 |
| C | VAL83 |
| C | THR111 |
| C | ILE159 |
| C | GLY160 |
| C | GLY162 |
| C | ARG163 |
| C | ILE164 |
| C | THR183 |
| C | GLY184 |
| C | ARG185 |
| C | ARG188 |
| C | ALA215 |
| C | CYS216 |
| site_id | AC9 |
| Number of Residues | 23 |
| Details | BINDING SITE FOR RESIDUE NDP D 2004 |
| Chain | Residue |
| D | VAL83 |
| D | THR111 |
| D | GLY162 |
| D | ARG163 |
| D | ILE164 |
| D | GLY184 |
| D | ARG185 |
| D | ARG188 |
| D | ALA215 |
| D | CYS216 |
| D | SER217 |
| D | THR222 |
| D | ILE243 |
| D | SER244 |
| D | ARG245 |
| D | ASP269 |
| D | HIS293 |
| D | GLY295 |
| D | SER296 |
| D | HOH2014 |
| D | HOH2096 |
| D | HOH2104 |
| D | HOH2107 |
| site_id | BC1 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE DGY A 3001 |
| Chain | Residue |
| A | LEU59 |
| A | SER82 |
| A | VAL83 |
| A | GLY84 |
| A | LEU107 |
| A | ARG245 |
| A | HIS293 |
| A | SER296 |
| A | NDP2001 |
| B | TRP141 |
| site_id | BC2 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE DGY C 3002 |
| Chain | Residue |
| C | LEU59 |
| C | SER82 |
| C | VAL83 |
| C | GLY84 |
| C | LEU107 |
| C | ARG245 |
| C | HIS293 |
| C | SER296 |
| C | NDP2003 |
| D | TRP141 |
Functional Information from PROSITE/UniProt
| site_id | PS00671 |
| Number of Residues | 17 |
| Details | D_2_HYDROXYACID_DH_3 D-isomer specific 2-hydroxyacid dehydrogenases signature 3. MKeTaVFINiSRGdVVN |
| Chain | Residue | Details |
| A | MET234-ASN250 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | ACT_SITE: Proton donor => ECO:0000305|PubMed:16756993 |
| Chain | Residue | Details |
| A | HIS293 | |
| B | HIS293 | |
| C | HIS293 | |
| D | HIS293 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 36 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:16756993 |
| Chain | Residue | Details |
| A | VAL83 | |
| B | VAL83 | |
| B | GLY162 | |
| B | ARG185 | |
| B | SER217 | |
| B | ILE243 | |
| B | ARG245 | |
| B | ASP269 | |
| B | HIS293 | |
| B | GLY295 | |
| C | VAL83 | |
| A | GLY162 | |
| C | GLY162 | |
| C | ARG185 | |
| C | SER217 | |
| C | ILE243 | |
| C | ARG245 | |
| C | ASP269 | |
| C | HIS293 | |
| C | GLY295 | |
| D | VAL83 | |
| D | GLY162 | |
| A | ARG185 | |
| D | ARG185 | |
| D | SER217 | |
| D | ILE243 | |
| D | ARG245 | |
| D | ASP269 | |
| D | HIS293 | |
| D | GLY295 | |
| A | SER217 | |
| A | ILE243 | |
| A | ARG245 | |
| A | ASP269 | |
| A | HIS293 | |
| A | GLY295 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | SITE: Raises pKa of active site His => ECO:0000305|PubMed:16756993 |
| Chain | Residue | Details |
| A | GLU274 | |
| B | GLU274 | |
| C | GLU274 | |
| D | GLU274 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 8 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| A | SER36 | |
| A | SER272 | |
| B | SER36 | |
| B | SER272 | |
| C | SER36 | |
| C | SER272 | |
| D | SER36 | |
| D | SER272 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| A | THR298 | |
| B | THR298 | |
| C | THR298 | |
| D | THR298 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 5 |
| Details | Annotated By Reference To The Literature 1gdh |
| Chain | Residue | Details |
| A | ARG245 | |
| A | ASP269 | |
| A | GLU274 | |
| A | HIS293 | |
| A | ASP247 |
| site_id | CSA2 |
| Number of Residues | 5 |
| Details | Annotated By Reference To The Literature 1gdh |
| Chain | Residue | Details |
| B | ARG245 | |
| B | ASP269 | |
| B | GLU274 | |
| B | HIS293 | |
| B | ASP247 |
| site_id | CSA3 |
| Number of Residues | 5 |
| Details | Annotated By Reference To The Literature 1gdh |
| Chain | Residue | Details |
| C | ARG245 | |
| C | ASP269 | |
| C | GLU274 | |
| C | HIS293 | |
| C | ASP247 |
| site_id | CSA4 |
| Number of Residues | 5 |
| Details | Annotated By Reference To The Literature 1gdh |
| Chain | Residue | Details |
| D | ARG245 | |
| D | ASP269 | |
| D | GLU274 | |
| D | HIS293 | |
| D | ASP247 |
| site_id | CSA5 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1gdh |
| Chain | Residue | Details |
| A | GLU274 | |
| A | HIS293 |
| site_id | CSA6 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1gdh |
| Chain | Residue | Details |
| B | GLU274 | |
| B | HIS293 |
| site_id | CSA7 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1gdh |
| Chain | Residue | Details |
| C | GLU274 | |
| C | HIS293 |
| site_id | CSA8 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1gdh |
| Chain | Residue | Details |
| D | GLU274 | |
| D | HIS293 |
