SMTL ID : 6lpp.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 35 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.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, 2HG.3 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:W.46, A:A.148 Hydrogen bonds: 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:T.160, A:G.163, A:I.219, A:I.219, A:E.429, A:N.466 Water bridges: A:T.160, A:H.430 FAD.6: 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.7, 2HG.8 21 PLIP interactions: 21 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: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, 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
A

B
B

D-2-hydroxyglutarate dehydrogenase, mitochondrial

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