SMTL ID : 8w7f.1

Structure of Drosophila melanogaster L-2-hydroxyglutarate dehydrogenase bound with FAD and a sulfate ion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 8 residues within 4Å: Chain A: S.48, H.52, Y.249, L.259, H.262, P.275, R.353 Ligands: FAD.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.48, A:Y.249 Water bridges: A:R.353, A:R.353 Salt bridges: A:H.52, A:H.262, A:R.353 SO4.4: 8 residues within 4Å: Chain B: S.48, H.52, Y.249, L.259, H.262, P.275, R.353 Ligands: FAD.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.48, B:S.48 Salt bridges: B:H.52, B:H.262, B:R.353 SO4.7: 8 residues within 4Å: Chain C: S.48, H.52, Y.249, L.259, H.262, P.275, R.353 Ligands: FAD.8 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.48, C:Y.249 Water bridges: C:R.353, C:R.353 Salt bridges: C:H.52, C:H.262, C:R.353 SO4.10: 8 residues within 4Å: Chain D: S.48, H.52, Y.249, L.259, H.262, P.275, R.353 Ligands: FAD.11 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.48, D:S.48 Water bridges: D:L.259, D:R.353 Salt bridges: D:H.52, D:H.262, D:R.353

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

FAD.2: 36 residues within 4Å: Chain A: 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, W.149, F.171, N.172, 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 Ligands: SO4.1 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:N.47, A:R.353 Hydrogen bonds: A:G.10, A:G.11, A:I.12, A:V.13, A:G.14, A:K.35, A:H.42, A:Q.43, A:Q.43, A:Q.43, A:S.44, A:S.44, A:S.48, A:V.50, A:V.50, A:V.173, A:V.173, A:R.353, A:G.392, A:A.393, A:T.394, A:T.394 Water bridges: A:K.41, A:H.42, A:H.42 pi-Cation interactions: A:K.35, A:R.353 FAD.5: 36 residues within 4Å: Chain B: 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, W.149, F.171, N.172, 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 Ligands: SO4.4 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:N.47, B:R.353 Hydrogen bonds: B:G.10, B:G.11, B:V.13, B:K.35, B:H.42, B:Q.43, B:Q.43, B:S.44, B:S.44, B:S.48, B:V.50, B:V.50, B:V.173, B:V.173, B:G.392, B:A.393, B:T.394 Water bridges: B:G.14, B:G.14, B:K.35, B:K.41, B:H.42 pi-Cation interactions: B:K.35, B:R.353 FAD.8: 36 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, W.149, F.171, N.172, 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 Ligands: SO4.7 27 PLIP interactions: 27 interactions with chain C Hydrophobic interactions: C:N.47, C:R.353 Hydrogen bonds: C:G.10, C:G.11, C:I.12, C:V.13, C:G.14, C:K.35, C:H.42, C:Q.43, C:Q.43, C:Q.43, C:S.44, C:S.44, C:N.47, C:S.48, C:V.50, C:V.50, C:V.173, C:V.173, C:G.392, C:A.393, C:T.394 Water bridges: C:K.41, C:H.42 pi-Cation interactions: C:K.35, C:R.353 FAD.11: 36 residues within 4Å: Chain D: V.8, 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, V.352, R.353, P.391, G.392, A.393, T.394 Ligands: SO4.10 27 PLIP interactions: 27 interactions with chain D Hydrophobic interactions: D:N.47, D:R.353 Hydrogen bonds: D:I.12, D:V.13, D:G.14, D:K.35, D:H.42, D:Q.43, D:Q.43, D:Q.43, D:S.44, D:S.44, D:S.48, D:V.50, D:V.50, D:V.173, D:V.173, D:G.392, D:A.393, D:T.394, D:T.394 Water bridges: D:G.11, D:K.35, D:H.42, D:H.42 pi-Cation interactions: D:K.35, D:R.353

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

LMT.3: 20 residues within 4Å: Chain A: 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, G.316, E.319, K.322, A.332, K.335, Y.336 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.229, A:F.256, A:F.258, A:F.258, A:L.279, A:F.305, A:F.305 Hydrogen bonds: A:D.253, A:V.261, A:V.261, A:K.335, A:K.335 Water bridges: A:F.258, A:G.260, A:G.260, A:K.322, A:K.322 Salt bridges: A:K.322 LMT.6: 21 residues within 4Å: Chain B: E.99, P.250, V.251, P.252, D.253, F.256, F.258, G.260, V.261, L.279, F.305, M.308, Y.312, I.313, F.315, G.316, E.319, K.322, A.332, K.335, Y.336 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.256, B:F.258, B:L.279, B:F.305, B:Y.312, B:I.313, B:F.315, B:E.319 Hydrogen bonds: B:E.99, B:D.253, B:V.261, B:V.261, B:K.335, B:K.335, B:Y.336 Water bridges: B:K.322, B:K.322 Salt bridges: B:K.322 LMT.9: 21 residues within 4Å: Chain C: E.99, P.250, V.251, P.252, D.253, F.256, F.258, G.260, V.261, L.279, F.305, M.308, Y.312, I.313, F.315, G.316, E.319, K.322, A.332, K.335, Y.336 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:F.256, C:F.258, C:L.279, C:F.305, C:Y.312, C:I.313, C:F.315 Hydrogen bonds: C:D.253, C:V.261, C:V.261, C:K.335, C:K.335 Water bridges: C:D.253, C:F.258 Salt bridges: C:K.322 LMT.12: 20 residues within 4Å: Chain D: 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, F.315, G.316, E.319, K.322, A.332, K.335, Y.336 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:F.256, D:F.258, D:F.305, D:A.309, D:Y.312, D:F.315 Hydrogen bonds: D:D.253, D:V.261, D:V.261, D:K.335, D:K.335, D:Y.336 Salt bridges: D:K.322

Links

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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
A

B
B

C
C

D
D

FI05204p

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