1SC6
Crystal Structure of W139G D-3-Phosphoglycerate dehydrogenase complexed with NAD+
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004617 | molecular_function | phosphoglycerate dehydrogenase activity |
| A | 0005829 | cellular_component | cytosol |
| A | 0006564 | biological_process | L-serine biosynthetic process |
| A | 0008652 | biological_process | amino acid biosynthetic process |
| 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 | 0042802 | molecular_function | identical protein binding |
| A | 0047545 | molecular_function | (S)-2-hydroxyglutarate dehydrogenase activity |
| A | 0051287 | molecular_function | NAD binding |
| A | 0070403 | molecular_function | NAD+ binding |
| A | 0070404 | molecular_function | NADH binding |
| A | 0070905 | molecular_function | serine binding |
| A | 0120568 | molecular_function | (R)-2-hydroxyglutarate (NAD+) dehydrogenase activity |
| B | 0004617 | molecular_function | phosphoglycerate dehydrogenase activity |
| B | 0005829 | cellular_component | cytosol |
| B | 0006564 | biological_process | L-serine biosynthetic process |
| B | 0008652 | biological_process | amino acid biosynthetic process |
| 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 | 0042802 | molecular_function | identical protein binding |
| B | 0047545 | molecular_function | (S)-2-hydroxyglutarate dehydrogenase activity |
| B | 0051287 | molecular_function | NAD binding |
| B | 0070403 | molecular_function | NAD+ binding |
| B | 0070404 | molecular_function | NADH binding |
| B | 0070905 | molecular_function | serine binding |
| B | 0120568 | molecular_function | (R)-2-hydroxyglutarate (NAD+) dehydrogenase activity |
| C | 0004617 | molecular_function | phosphoglycerate dehydrogenase activity |
| C | 0005829 | cellular_component | cytosol |
| C | 0006564 | biological_process | L-serine biosynthetic process |
| C | 0008652 | biological_process | amino acid biosynthetic process |
| 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 | 0042802 | molecular_function | identical protein binding |
| C | 0047545 | molecular_function | (S)-2-hydroxyglutarate dehydrogenase activity |
| C | 0051287 | molecular_function | NAD binding |
| C | 0070403 | molecular_function | NAD+ binding |
| C | 0070404 | molecular_function | NADH binding |
| C | 0070905 | molecular_function | serine binding |
| C | 0120568 | molecular_function | (R)-2-hydroxyglutarate (NAD+) dehydrogenase activity |
| D | 0004617 | molecular_function | phosphoglycerate dehydrogenase activity |
| D | 0005829 | cellular_component | cytosol |
| D | 0006564 | biological_process | L-serine biosynthetic process |
| D | 0008652 | biological_process | amino acid biosynthetic process |
| 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 | 0042802 | molecular_function | identical protein binding |
| D | 0047545 | molecular_function | (S)-2-hydroxyglutarate dehydrogenase activity |
| D | 0051287 | molecular_function | NAD binding |
| D | 0070403 | molecular_function | NAD+ binding |
| D | 0070404 | molecular_function | NADH binding |
| D | 0070905 | molecular_function | serine binding |
| D | 0120568 | molecular_function | (R)-2-hydroxyglutarate (NAD+) dehydrogenase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE NAD A 2101 |
| Chain | Residue |
| A | PRO105 |
| A | ASP181 |
| A | ILE182 |
| A | LYS185 |
| A | HIS210 |
| A | VAL211 |
| A | PRO212 |
| A | SER216 |
| A | THR217 |
| A | ARG240 |
| A | HOH1616 |
| A | PHE106 |
| A | HOH1894 |
| A | ASN108 |
| A | THR109 |
| A | GLY158 |
| A | TYR159 |
| A | GLY160 |
| A | HIS161 |
| A | ILE162 |
| site_id | AC2 |
| Number of Residues | 25 |
| Details | BINDING SITE FOR RESIDUE NAD B 2102 |
| Chain | Residue |
| B | ILE84 |
| B | PRO105 |
| B | PHE106 |
| B | ASN108 |
| B | THR109 |
| B | GLY158 |
| B | TYR159 |
| B | GLY160 |
| B | HIS161 |
| B | ILE162 |
| B | ASP181 |
| B | ILE182 |
| B | LYS185 |
| B | HIS210 |
| B | VAL211 |
| B | PRO212 |
| B | SER216 |
| B | THR217 |
| B | SER239 |
| B | HOH1601 |
| B | HOH1671 |
| B | HOH1717 |
| B | HOH1871 |
| B | HOH1893 |
| B | HOH1958 |
| site_id | AC3 |
| Number of Residues | 22 |
| Details | BINDING SITE FOR RESIDUE NAD C 2103 |
| Chain | Residue |
| C | PRO105 |
| C | PHE106 |
| C | ASN108 |
| C | THR109 |
| C | GLY158 |
| C | TYR159 |
| C | GLY160 |
| C | HIS161 |
| C | ILE162 |
| C | ASP181 |
| C | ILE182 |
| C | LYS185 |
| C | HIS210 |
| C | VAL211 |
| C | PRO212 |
| C | SER216 |
| C | THR217 |
| C | HOH1611 |
| C | HOH1637 |
| C | HOH1869 |
| C | HOH1900 |
| C | HOH1942 |
| site_id | AC4 |
| Number of Residues | 22 |
| Details | BINDING SITE FOR RESIDUE NAD D 2104 |
| Chain | Residue |
| D | PRO105 |
| D | PHE106 |
| D | ASN108 |
| D | THR109 |
| D | GLY158 |
| D | TYR159 |
| D | GLY160 |
| D | HIS161 |
| D | ILE162 |
| D | TYR180 |
| D | ASP181 |
| D | ILE182 |
| D | LYS185 |
| D | HIS210 |
| D | VAL211 |
| D | PRO212 |
| D | SER216 |
| D | THR217 |
| D | SER239 |
| D | HOH1600 |
| D | HOH1732 |
| D | HOH1943 |
Functional Information from PROSITE/UniProt
| site_id | PS00065 |
| Number of Residues | 28 |
| Details | D_2_HYDROXYACID_DH_1 D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. LGIIGyGHIGtqlgilaeslgmy.VYfYD |
| Chain | Residue | Details |
| A | LEU154-ASP181 |
| site_id | PS00670 |
| Number of Residues | 23 |
| Details | D_2_HYDROXYACID_DH_2 D-isomer specific 2-hydroxyacid dehydrogenases signature 2. LLnmSDVVsLHvPenpsTknMmG |
| Chain | Residue | Details |
| A | LEU200-GLY222 |
| site_id | PS00671 |
| Number of Residues | 17 |
| Details | D_2_HYDROXYACID_DH_3 D-isomer specific 2-hydroxyacid dehydrogenases signature 3. MKpGsLLINaSRGtVVD |
| Chain | Residue | Details |
| A | MSE229-ASP245 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 8 |
| Details | Active site: {} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | Active site: {"description":"Proton donor"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 32 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"7719856","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1psd |
| Chain | Residue | Details |
| A | HIS292 |
| site_id | CSA2 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1psd |
| Chain | Residue | Details |
| B | HIS292 |
| site_id | MCSA1 |
| Number of Residues | 2 |
| Details | M-CSA 785 |
| Chain | Residue | Details |
| A | LEU289 | electrostatic stabiliser |
| A | LEU312 | proton acceptor, proton donor |
| site_id | MCSA2 |
| Number of Residues | 2 |
| Details | M-CSA 785 |
| Chain | Residue | Details |
| B | LEU289 | electrostatic stabiliser |
| B | LEU312 | proton acceptor, proton donor |
| site_id | MCSA3 |
| Number of Residues | 2 |
| Details | M-CSA 785 |
| Chain | Residue | Details |
| C | LEU289 | electrostatic stabiliser |
| C | LEU312 | proton acceptor, proton donor |
| site_id | MCSA4 |
| Number of Residues | 2 |
| Details | M-CSA 785 |
| Chain | Residue | Details |
| D | LEU289 | electrostatic stabiliser |
| D | LEU312 | proton acceptor, proton donor |
