SMTL ID : 7y0b.1

Crystal structure of human short-chain acyl-CoA dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 30 residues within 4Å: Chain A: F.130, L.132, S.133, N.137, G.138, S.139, W.163, I.164, T.165, K.208, T.216, I.365, I.368, Y.369, E.370, T.372, E.374, I.375, L.378 Chain B: R.275, F.278, L.282, L.285, V.287, I.288, Q.343, I.344, G.346, G.347 Chain C: Q.286 28 PLIP interactions: 19 interactions with chain A, 8 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: A:W.163, A:K.208, A:T.216, A:I.365 Hydrogen bonds: A:F.130, A:L.132, A:S.133, A:S.133, A:G.138, A:S.139, A:S.139, A:T.165, A:E.370, A:G.371, A:T.372, A:T.372, B:Q.343, B:G.347, C:Q.286 Water bridges: A:D.140, A:T.372, B:R.275, B:R.275, B:M.348, B:M.348 pi-Stacking: A:Y.369 Salt bridges: B:R.275, B:R.275 FAD.2: 31 residues within 4Å: Chain A: R.275, F.278, L.282, L.285, V.287, I.288, Q.343, I.344, G.346, G.347 Chain B: F.130, L.132, S.133, N.137, G.138, S.139, W.163, I.164, T.165, K.208, T.216, I.365, I.368, Y.369, E.370, G.371, T.372, E.374, I.375, L.378 Chain D: Q.286 29 PLIP interactions: 19 interactions with chain B, 9 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: B:W.163, B:K.208, B:T.216 Hydrogen bonds: B:F.130, B:L.132, B:S.133, B:S.133, B:G.138, B:S.139, B:S.139, B:T.165, B:T.165, B:I.368, B:E.370, B:G.371, B:T.372, B:T.372, A:Q.343, A:G.347, D:Q.286 Water bridges: B:W.163, A:R.275, A:R.275, A:R.275, A:M.348, A:M.348 pi-Stacking: B:Y.369 Salt bridges: A:R.275, A:R.275 FAD.4: 28 residues within 4Å: Chain A: Q.286 Chain C: F.130, L.132, S.133, G.138, S.139, W.163, I.164, T.165, K.208, T.216, I.365, I.368, Y.369, E.370, T.372, E.374, I.375, L.378 Chain D: R.275, F.278, L.282, L.285, I.288, Q.343, I.344, G.346, G.347 28 PLIP interactions: 20 interactions with chain C, 7 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: C:W.163, C:K.208, C:T.216, C:I.365 Hydrogen bonds: C:F.130, C:L.132, C:S.133, C:S.133, C:G.138, C:S.139, C:S.139, C:T.165, C:E.370, C:G.371, C:T.372, C:E.374, D:Q.343, D:G.347, A:Q.286 Water bridges: C:N.137, C:G.138, C:T.372, D:Y.271, D:R.275, D:M.348 pi-Stacking: C:Y.369 Salt bridges: D:R.275, D:R.275 FAD.5: 26 residues within 4Å: Chain B: Q.286 Chain C: R.275, F.278, L.282, L.285, I.288, Q.343, I.344, G.346, G.347 Chain D: F.130, L.132, S.133, G.138, S.139, W.163, I.164, T.165, K.208, I.365, I.368, Y.369, E.370, T.372, E.374, L.378 25 PLIP interactions: 16 interactions with chain D, 8 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: D:W.163, D:K.208, D:I.365 Hydrogen bonds: D:F.130, D:L.132, D:S.133, D:S.133, D:S.139, D:S.139, D:T.165, D:E.370, D:T.372, D:E.374, C:Q.343, C:G.347, B:Q.286 Water bridges: D:G.138, D:D.140, C:Y.271, C:R.275, C:R.275, C:M.348 pi-Stacking: D:Y.369 Salt bridges: C:R.275, C:R.275

1 x 7R3: (2S,3R,4R,5S,6R)-2-[4-chloranyl-3-[[4-[(3S)-oxolan-3-yl]oxyphenyl]methyl]phenyl]-6-(hydroxymethyl)oxane-3,4,5-triol(Non-covalent)

7R3.3: 11 residues within 4Å: Chain A: K.40, M.348, T.352, E.353 Chain B: P.135, A.162, W.163, K.204, E.206, D.207, N.218 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:K.204, A:E.353 Hydrogen bonds: B:W.163, B:K.204, B:N.218, A:T.352, A:E.353 Water bridges: A:R.275

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Y. et al., Crystal structure of human short-chain acyl-coA dehydrogenase. To Be Published

Release Date

2023-07-05

Peptides

Short-chain specific acyl-CoA dehydrogenase, mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Short-chain specific acyl-CoA dehydrogenase, mitochondrial

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