SMTL ID : 6lpx.1

Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with 2-oxoglutarate (2-OG)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 36 residues within 4Å: Chain A: W.46, P.82, Q.83, G.84, G.85, N.86, T.87, G.88, M.89, G.92, S.93, T.104, L.146, G.147, A.148, C.152, H.153, G.155, G.156, N.157, A.159, T.160, A.162, G.163, G.164, E.213, G.214, G.217, I.218, I.219, H.388, E.429, H.430, N.466 Ligands: ZN.2, AKG.3 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:W.46, A:A.148 Hydrogen bonds: A:N.81, A:G.84, A:G.85, A:N.86, A:T.87, A:T.87, A:T.87, A:T.87, A:G.88, A:G.92, A:S.93, A:S.93, A:G.147, A:H.153, A:N.157, A:T.160, A:G.163, A:I.219, A:I.219, A:E.429, A:N.466 Water bridges: A:G.156, A:G.156 pi-Cation interactions: A:H.430 FAD.4: 36 residues within 4Å: Chain B: W.46, P.82, Q.83, G.84, G.85, N.86, T.87, G.88, M.89, G.92, S.93, T.104, A.124, L.146, G.147, A.148, C.152, H.153, G.156, N.157, A.159, T.160, A.162, G.163, G.164, E.213, G.214, G.217, I.218, I.219, H.388, E.429, H.430, N.466 Ligands: ZN.5, AKG.6 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:W.46, B:A.148 Hydrogen bonds: B:G.84, B:G.85, B:N.86, B:T.87, B:T.87, B:T.87, B:G.88, B:G.92, B:S.93, B:S.93, B:G.147, B:H.153, B:G.163, B:I.219, B:I.219, B:E.429, B:N.466 Water bridges: B:M.89, B:T.104, B:G.156, B:T.160, B:H.430

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.388, H.395, E.429 Ligands: FAD.1, AKG.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.388, A:H.395, A:E.429 ZN.5: 5 residues within 4Å: Chain B: H.388, H.395, E.429 Ligands: FAD.4, AKG.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.388, B:H.395, B:E.429

2 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.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 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.344 Hydrogen bonds: A:T.344, A:T.344, A:N.397 Salt bridges: A:R.340, A:K.355, A:H.388, A:H.395, A:H.395, A:H.430 AKG.6: 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.4, ZN.5 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:T.344, B:T.344, B:T.344, B:Y.386, B:N.397 Salt bridges: B:R.340, B:K.355, B:H.388, B:H.395, B:H.395, B:H.430

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
A

B
B

D-2-hydroxyglutarate dehydrogenase, mitochondrial

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