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 | 0006089 | biological_process | lactate metabolic process |
| 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 | 0031648 | biological_process | protein destabilization |
| 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 |
| A | 1901275 | biological_process | tartrate metabolic process |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0005739 | cellular_component | mitochondrion |
| B | 0005759 | cellular_component | mitochondrial matrix |
| B | 0006089 | biological_process | lactate metabolic process |
| 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 | 0031648 | biological_process | protein destabilization |
| 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 |
| B | 1901275 | biological_process | tartrate metabolic process |
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 | 358 |
| Details | Domain: {"description":"FAD-binding PCMH-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00718","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"33431826","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"6LPQ","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 6 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"33431826","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"33431826","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"6LPP","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"Q8CIM3","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
