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 | 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 |
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 | 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 |
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 | 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 |
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 | 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 |
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 | ACT_SITE: |
Chain | Residue | Details |
A | GLY241 | |
A | PRO270 | |
B | GLY241 | |
B | PRO270 | |
C | GLY241 | |
C | PRO270 | |
D | GLY241 | |
D | PRO270 |
site_id | SWS_FT_FI2 |
Number of Residues | 4 |
Details | ACT_SITE: Proton donor |
Chain | Residue | Details |
A | ILE293 | |
B | ILE293 | |
C | ILE293 | |
D | ILE293 |
site_id | SWS_FT_FI3 |
Number of Residues | 20 |
Details | BINDING: BINDING => ECO:0000269|PubMed:7719856 |
Chain | Residue | Details |
A | ILE162 | |
B | ILE293 | |
C | ILE162 | |
C | ILE182 | |
C | SER239 | |
C | VAL265 | |
C | ILE293 | |
D | ILE162 | |
D | ILE182 | |
D | SER239 | |
D | VAL265 | |
A | ILE182 | |
D | ILE293 | |
A | SER239 | |
A | VAL265 | |
A | ILE293 | |
B | ILE162 | |
B | ILE182 | |
B | SER239 | |
B | VAL265 |
Catalytic Information from CSA
site_id | MCSA1 |
Number of Residues | 2 |
Details | M-CSA 785 |
Chain | Residue | Details |
A | PRO270 | electrostatic stabiliser |
A | ILE293 | proton acceptor, proton donor |
site_id | MCSA2 |
Number of Residues | 2 |
Details | M-CSA 785 |
Chain | Residue | Details |
B | PRO270 | electrostatic stabiliser |
B | ILE293 | proton acceptor, proton donor |
site_id | MCSA3 |
Number of Residues | 2 |
Details | M-CSA 785 |
Chain | Residue | Details |
C | PRO270 | electrostatic stabiliser |
C | ILE293 | proton acceptor, proton donor |
site_id | MCSA4 |
Number of Residues | 2 |
Details | M-CSA 785 |
Chain | Residue | Details |
D | PRO270 | electrostatic stabiliser |
D | ILE293 | proton acceptor, proton donor |