SMTL ID : 8w75.1

Structure of Drosophila melanogaster L-2-hydroxyglutarate dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 35 residues within 4Å: Chain A: G.9, G.11, I.12, V.13, G.14, L.33, E.34, K.35, E.36, H.42, Q.43, S.44, H.46, N.47, S.48, G.49, V.50, H.52, W.149, F.171, N.172, V.173, C.206, G.207, G.208, Q.210, L.214, Y.233, P.275, V.352, R.353, P.391, G.392, A.393, T.394 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:N.47, A:P.275, A:R.353 Hydrogen bonds: A:G.9, A:G.10, A:V.13, A:G.14, A:K.35, A:H.42, A:Q.43, A:Q.43, A:S.44, A:S.48, A:V.50, A:V.50, A:V.173, A:V.173, A:G.392, A:A.393, A:T.394, A:T.394 FAD.3: 37 residues within 4Å: Chain B: V.8, G.9, G.10, G.11, I.12, V.13, G.14, L.33, E.34, K.35, E.36, H.42, Q.43, S.44, H.46, N.47, S.48, G.49, V.50, H.52, W.149, F.171, N.172, V.173, C.206, G.207, G.208, Q.210, L.214, Y.233, G.351, V.352, R.353, P.391, G.392, A.393, T.394 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:N.47, B:R.353 Hydrogen bonds: B:G.10, B:G.11, B:I.12, B:V.13, B:G.14, B:K.35, B:H.42, B:Q.43, B:Q.43, B:Q.43, B:S.44, B:S.48, B:G.49, B:V.50, B:V.50, B:V.173, B:V.173, B:G.392, B:A.393, B:T.394 pi-Cation interactions: B:K.35, B:R.353 FAD.5: 34 residues within 4Å: Chain C: V.8, G.9, G.10, G.11, I.12, V.13, L.33, E.34, K.35, E.36, H.42, Q.43, S.44, H.46, N.47, S.48, G.49, V.50, H.52, F.171, V.173, C.206, G.207, G.208, Q.210, L.214, Y.233, G.351, V.352, R.353, P.391, G.392, A.393, T.394 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:N.47, C:R.353 Hydrogen bonds: C:G.10, C:G.11, C:V.13, C:K.35, C:H.42, C:Q.43, C:Q.43, C:S.44, C:S.48, C:G.49, C:V.50, C:V.50, C:V.173, C:V.173, C:G.392, C:A.393, C:T.394 FAD.7: 33 residues within 4Å: Chain D: V.8, G.9, G.10, G.11, I.12, V.13, L.33, E.34, K.35, E.36, H.42, Q.43, S.44, H.46, N.47, S.48, G.49, V.50, H.52, F.171, V.173, C.206, G.207, G.208, Q.210, L.214, Y.233, V.352, R.353, P.391, G.392, A.393, T.394 24 PLIP interactions: 24 interactions with chain D Hydrophobic interactions: D:Q.43, D:N.47, D:R.353 Hydrogen bonds: D:G.9, D:G.10, D:I.12, D:V.13, D:K.35, D:H.42, D:Q.43, D:Q.43, D:S.44, D:S.44, D:N.47, D:V.50, D:V.50, D:H.52, D:V.173, D:V.173, D:G.208, D:G.392, D:A.393, D:T.394 pi-Cation interactions: D:K.35

4 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.2: 19 residues within 4Å: Chain A: F.229, P.250, V.251, P.252, D.253, F.258, G.260, V.261, A.277, L.279, F.305, M.308, A.309, Y.312, F.315, G.316, E.319, A.332, Y.336 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.229, A:F.258, A:L.279, A:F.305, A:A.309, A:F.315, A:E.319 Hydrogen bonds: A:D.253, A:V.261, A:V.261 LMT.4: 18 residues within 4Å: Chain B: P.250, V.251, P.252, D.253, F.256, F.258, G.260, V.261, A.277, F.305, M.308, A.309, Y.312, I.313, G.316, E.319, A.332, Y.336 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.256, B:F.258, B:A.277, B:F.305, B:A.309, B:Y.312, B:E.319 Hydrogen bonds: B:D.253, B:V.261, B:V.261, B:Y.336 LMT.6: 21 residues within 4Å: Chain C: E.99, F.229, P.250, V.251, P.252, D.253, F.256, F.258, G.260, V.261, A.277, L.279, F.305, M.308, Y.312, I.313, G.316, E.319, K.322, A.332, Y.336 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:F.229, C:F.256, C:F.258, C:F.258, C:A.277, C:L.279, C:F.305, C:Y.312, C:I.313, C:E.319 Hydrogen bonds: C:D.253, C:V.261, C:V.261 Salt bridges: C:K.322 LMT.8: 20 residues within 4Å: Chain D: F.229, P.250, V.251, P.252, D.253, F.256, F.258, G.260, V.261, A.277, L.279, F.305, M.308, Y.312, I.313, F.315, G.316, E.319, A.332, Y.336 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:F.229, D:F.256, D:F.258, D:F.258, D:A.277, D:L.279, D:F.305, D:Y.312, D:I.313, D:F.315, D:E.319 Hydrogen bonds: D:D.253, D:V.261, D:V.261, D:Y.336

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, J. et al., Structure and biochemical characterization of l-2-hydroxyglutarate dehydrogenase and its role in the pathogenesis of l-2-hydroxyglutaric aciduria. J.Biol.Chem. (2023)

Release Date

2023-11-29

Peptides

FI05204p: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

C
B

D
C

FI05204p

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