SMTL ID : 7y0a.1

Crystal structure of human short-chain acyl-CoA dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 33 residues within 4Å: Chain A: F.130, L.132, S.133, N.137, G.138, S.139, A.162, W.163, I.164, T.165, K.208, I.211, 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, Y.350 Chain C: Q.286 31 PLIP interactions: 21 interactions with chain A, 9 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: A:W.163, A:K.208, A:I.211, A:T.216, A:I.365, A:Y.369, B:Y.350, B:Y.350 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: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:E.134, B:R.275, B:R.275, B:R.275 pi-Stacking: A:Y.369 Salt bridges: B:R.275, B:R.275 FAD.3: 33 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, Y.350 Chain B: F.130, L.132, S.133, N.137, G.138, S.139, W.163, I.164, T.165, K.208, I.211, T.216, I.365, I.368, Y.369, E.370, G.371, T.372, E.374, I.375, L.378 Chain D: Q.286 34 PLIP interactions: 23 interactions with chain B, 10 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: B:W.163, B:K.208, B:I.211, B:T.216, B:I.365, B:Y.369, B:Y.369, A:Y.350, A:Y.350 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:E.370, B:G.371, B:T.372, B:T.372, B:E.374, A:Q.343, A:G.347, D:Q.286 Water bridges: B:N.137, B:W.163, A:R.275, A:R.275, A:M.348, A:M.348 Salt bridges: A:R.275, A:R.275 FAD.6: 32 residues within 4Å: Chain A: Q.286 Chain C: F.130, L.132, S.133, N.137, G.138, S.139, A.162, W.163, I.164, T.165, K.208, I.211, 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, Y.350 30 PLIP interactions: 19 interactions with chain C, 10 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: C:W.163, C:K.208, C:I.211, C:T.216, C:I.365, D:Y.350 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:W.163, D:Y.271, D:R.275, D:R.275, D:R.275, D:M.348 pi-Stacking: C:Y.369 Salt bridges: D:R.275, D:R.275 FAD.7: 31 residues within 4Å: Chain B: Q.286 Chain C: R.275, F.278, L.282, L.285, V.287, I.288, Q.343, I.344, G.346, G.347, Y.350 Chain D: F.130, L.132, S.133, N.137, G.138, S.139, W.163, I.164, T.165, K.208, I.211, T.216, I.365, I.368, Y.369, E.370, T.372, E.374, L.378 29 PLIP interactions: 21 interactions with chain D, 1 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: D:W.163, D:K.208, D:I.211, D:T.216, D:I.365, D:Y.369, D:Y.369, C:Y.350 Hydrogen bonds: D:F.130, D:L.132, D:S.133, D:S.133, D:S.139, D:S.139, D:W.163, D:T.165, D:E.370, D:T.372, D:E.374, B:Q.286, C:Q.343, C:G.347 Water bridges: D:G.138, D:D.140, C:R.275, C:R.275 pi-Stacking: D:Y.369 Salt bridges: C:R.275, C:R.275

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 7 residues within 4Å: Chain A: P.135, A.162, W.163, E.206, N.218 Chain B: M.348, E.353 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.218 Water bridges: A:P.135, A:W.163 FMT.4: 7 residues within 4Å: Chain A: M.348, E.353 Chain B: P.135, A.162, W.163, E.206, N.218 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.206, B:N.218 FMT.5: 5 residues within 4Å: Chain C: P.135, A.162, W.163, E.206, N.218 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.206, C:E.206, C:N.218 Water bridges: C:W.163 FMT.8: 6 residues within 4Å: Chain C: E.353 Chain D: P.135, A.162, W.163, E.206, N.218 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:E.206, D:N.218, C:E.353 Water bridges: D:W.163

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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