- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.65 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
- 2 x ZN: ZINC ION(Non-covalent)
ZN.2: 5 residues within 4Å:- Chain A: H.388, H.395, E.429
- Ligands: FAD.1, 2HG.3
3 PLIP interactions:3 interactions with chain A- Metal complexes: A:H.388, A:H.395, A:E.429
ZN.7: 5 residues within 4Å:- Chain B: H.388, H.395, E.429
- Ligands: FAD.6, 2HG.8
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:H.388, B:H.395, B:E.429
- 2 x 2HG: (2R)-2-hydroxypentanedioic acid(Non-covalent)
2HG.3: 12 residues within 4Å:- Chain A: M.89, R.340, T.344, K.355, Y.386, H.388, H.395, N.397, E.429, H.430
- Ligands: FAD.1, ZN.2
13 PLIP interactions:13 interactions with chain A- Hydrophobic interactions: A:H.395
- Hydrogen bonds: A:T.344, A:T.344, A:Y.386, A:N.397
- Water bridges: A:H.395, A:L.396
- Salt bridges: A:R.340, A:K.355, A:H.388, A:H.395, A:H.395, A:H.430
2HG.8: 12 residues within 4Å:- Chain B: M.89, R.340, T.344, K.355, Y.386, H.388, H.395, N.397, E.429, H.430
- Ligands: FAD.6, ZN.7
13 PLIP interactions:13 interactions with chain B- Hydrophobic interactions: B:H.395
- Hydrogen bonds: B:T.344, B:T.344, B:T.344, B:Y.386, B:N.397
- Water bridges: B:G.147
- Salt bridges: B:R.340, B:K.355, B:H.388, B:H.395, B:H.395, B:H.430
- 7 x GOL: GLYCEROL(Non-functional Binders)
GOL.4: 2 residues within 4Å:- Chain A: K.381, H.382
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Q.273, A:D.350, A:K.381
GOL.5: 1 residues within 4Å:- Chain A: H.72
No protein-ligand interaction detected (PLIP)GOL.9: 1 residues within 4Å:- Chain B: H.74
No protein-ligand interaction detected (PLIP)GOL.10: 7 residues within 4Å:- Chain B: D.145, K.149, R.166, E.295, W.337, E.341
- Ligands: GOL.11
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:D.145, B:K.149, B:R.166, B:E.295, B:E.341
GOL.11: 8 residues within 4Å:- Chain B: I.141, R.166, Y.170, P.230, S.262, E.295, S.297
- Ligands: GOL.10
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:R.166, B:Y.170, B:Y.170, B:S.297, B:S.297
GOL.12: 4 residues within 4Å:- Chain B: H.379, S.404, S.406, L.407
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:H.379, B:S.404, B:S.404, B:L.407
GOL.13: 3 residues within 4Å:- Chain B: L.274, K.381, H.382
No protein-ligand interaction detected (PLIP)- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Yang, J. et al., Structure, substrate specificity, and catalytic mechanism of human D-2-HGDH and insights into pathogenicity of disease-associated mutations. Cell Discov (2021)
- Release Date
- 2021-01-13
- Peptides
- D-2-hydroxyglutarate dehydrogenase, mitochondrial: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.65 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
- 2 x ZN: ZINC ION(Non-covalent)
- 2 x 2HG: (2R)-2-hydroxypentanedioic acid(Non-covalent)
- 7 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Yang, J. et al., Structure, substrate specificity, and catalytic mechanism of human D-2-HGDH and insights into pathogenicity of disease-associated mutations. Cell Discov (2021)
- Release Date
- 2021-01-13
- Peptides
- D-2-hydroxyglutarate dehydrogenase, mitochondrial: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B