6LPP
Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with D-2-hydroxyglutarate (D-2-HG)
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0003824 | molecular_function | catalytic activity |
A | 0005739 | cellular_component | mitochondrion |
A | 0005759 | cellular_component | mitochondrial matrix |
A | 0006103 | biological_process | 2-oxoglutarate metabolic process |
A | 0006108 | biological_process | malate metabolic process |
A | 0008270 | molecular_function | zinc ion binding |
A | 0010042 | biological_process | response to manganese ion |
A | 0010043 | biological_process | response to zinc ion |
A | 0016491 | molecular_function | oxidoreductase activity |
A | 0019538 | biological_process | protein metabolic process |
A | 0032025 | biological_process | response to cobalt ion |
A | 0032026 | biological_process | response to magnesium ion |
A | 0046872 | molecular_function | metal ion binding |
A | 0050660 | molecular_function | flavin adenine dinucleotide binding |
A | 0051592 | biological_process | response to calcium ion |
A | 0051990 | molecular_function | (R)-2-hydroxyglutarate dehydrogenase activity |
A | 0071949 | molecular_function | FAD binding |
B | 0003824 | molecular_function | catalytic activity |
B | 0005739 | cellular_component | mitochondrion |
B | 0005759 | cellular_component | mitochondrial matrix |
B | 0006103 | biological_process | 2-oxoglutarate metabolic process |
B | 0006108 | biological_process | malate metabolic process |
B | 0008270 | molecular_function | zinc ion binding |
B | 0010042 | biological_process | response to manganese ion |
B | 0010043 | biological_process | response to zinc ion |
B | 0016491 | molecular_function | oxidoreductase activity |
B | 0019538 | biological_process | protein metabolic process |
B | 0032025 | biological_process | response to cobalt ion |
B | 0032026 | biological_process | response to magnesium ion |
B | 0046872 | molecular_function | metal ion binding |
B | 0050660 | molecular_function | flavin adenine dinucleotide binding |
B | 0051592 | biological_process | response to calcium ion |
B | 0051990 | molecular_function | (R)-2-hydroxyglutarate dehydrogenase activity |
B | 0071949 | molecular_function | FAD binding |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 31 |
Details | binding site for residue FAD A 601 |
Chain | Residue |
A | TRP92 |
A | SER139 |
A | LEU192 |
A | ALA194 |
A | CYS198 |
A | HIS199 |
A | GLY202 |
A | ASN203 |
A | ALA205 |
A | THR206 |
A | ALA208 |
A | PRO128 |
A | GLY209 |
A | GLY210 |
A | GLU259 |
A | GLY260 |
A | ILE265 |
A | GLU475 |
A | HIS476 |
A | ASN512 |
A | ZN602 |
A | 2HG603 |
A | GLY130 |
A | HOH714 |
A | HOH736 |
A | GLY131 |
A | ASN132 |
A | THR133 |
A | GLY134 |
A | MET135 |
A | GLY138 |
site_id | AC2 |
Number of Residues | 5 |
Details | binding site for residue ZN A 602 |
Chain | Residue |
A | HIS434 |
A | HIS441 |
A | GLU475 |
A | FAD601 |
A | 2HG603 |
site_id | AC3 |
Number of Residues | 13 |
Details | binding site for residue 2HG A 603 |
Chain | Residue |
A | ARG386 |
A | THR390 |
A | LYS401 |
A | TYR432 |
A | HIS434 |
A | HIS441 |
A | ASN443 |
A | GLU475 |
A | HIS476 |
A | FAD601 |
A | ZN602 |
A | HOH706 |
A | HOH712 |
site_id | AC4 |
Number of Residues | 2 |
Details | binding site for residue GOL A 604 |
Chain | Residue |
A | LYS427 |
A | HIS428 |
site_id | AC5 |
Number of Residues | 1 |
Details | binding site for residue GOL A 605 |
Chain | Residue |
A | HIS118 |
site_id | AC6 |
Number of Residues | 33 |
Details | binding site for residue FAD B 601 |
Chain | Residue |
B | TRP92 |
B | PRO128 |
B | GLY130 |
B | GLY131 |
B | ASN132 |
B | THR133 |
B | GLY134 |
B | MET135 |
B | GLY138 |
B | SER139 |
B | LEU192 |
B | ALA194 |
B | CYS198 |
B | HIS199 |
B | GLY202 |
B | ASN203 |
B | ALA205 |
B | THR206 |
B | ALA208 |
B | GLY209 |
B | GLY210 |
B | GLU259 |
B | GLY260 |
B | GLY263 |
B | ILE265 |
B | GLU475 |
B | HIS476 |
B | ASN512 |
B | ZN602 |
B | 2HG603 |
B | HOH708 |
B | HOH716 |
B | HOH725 |
site_id | AC7 |
Number of Residues | 5 |
Details | binding site for residue ZN B 602 |
Chain | Residue |
B | HIS434 |
B | HIS441 |
B | GLU475 |
B | FAD601 |
B | 2HG603 |
site_id | AC8 |
Number of Residues | 12 |
Details | binding site for residue 2HG B 603 |
Chain | Residue |
B | FAD601 |
B | ZN602 |
B | HOH709 |
B | ARG386 |
B | THR390 |
B | LYS401 |
B | TYR432 |
B | HIS434 |
B | HIS441 |
B | ASN443 |
B | GLU475 |
B | HIS476 |
site_id | AC9 |
Number of Residues | 1 |
Details | binding site for residue GOL B 604 |
Chain | Residue |
B | HIS120 |
site_id | AD1 |
Number of Residues | 7 |
Details | binding site for residue GOL B 605 |
Chain | Residue |
B | ASP191 |
B | LYS195 |
B | ARG212 |
B | GLU341 |
B | TRP383 |
B | GLU387 |
B | GOL606 |
site_id | AD2 |
Number of Residues | 7 |
Details | binding site for residue GOL B 606 |
Chain | Residue |
B | ILE187 |
B | ARG212 |
B | TYR216 |
B | PRO276 |
B | GLU341 |
B | SER343 |
B | GOL605 |
site_id | AD3 |
Number of Residues | 4 |
Details | binding site for residue GOL B 607 |
Chain | Residue |
B | HIS425 |
B | SER450 |
B | SER452 |
B | LEU453 |
site_id | AD4 |
Number of Residues | 2 |
Details | binding site for residue GOL B 608 |
Chain | Residue |
B | LYS427 |
B | HIS428 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 8 |
Details | BINDING: BINDING => ECO:0000269|PubMed:33431826, ECO:0007744|PDB:6LPQ |
Chain | Residue | Details |
A | ARG386 | |
A | THR390 | |
A | LYS401 | |
A | HIS476 | |
B | ARG386 | |
B | THR390 | |
B | LYS401 | |
B | HIS476 |
site_id | SWS_FT_FI2 |
Number of Residues | 6 |
Details | BINDING: BINDING => ECO:0000269|PubMed:33431826 |
Chain | Residue | Details |
A | HIS434 | |
A | HIS441 | |
A | GLU475 | |
B | HIS434 | |
B | HIS441 | |
B | GLU475 |
site_id | SWS_FT_FI3 |
Number of Residues | 2 |
Details | BINDING: BINDING => ECO:0000269|PubMed:33431826, ECO:0007744|PDB:6LPP |
Chain | Residue | Details |
A | ASN443 | |
B | ASN443 |
site_id | SWS_FT_FI4 |
Number of Residues | 2 |
Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:Q8CIM3 |
Chain | Residue | Details |
A | LYS101 | |
B | LYS101 |