SMTL ID : 8sgs.1

human liver mitochondrial Short-chain specific acyl-CoA dehydrogenase

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

FAD.1: 28 residues within 4Å: Chain A: F.152, L.154, S.155, G.160, S.161, W.185, T.187, K.230, I.387, I.390, Y.391, G.393, T.394, E.396, I.397, L.400 Chain B: Y.293, R.297, F.300, L.304, L.307, Q.365, I.366, L.367, G.368, G.369 Chain C: Q.308 Ligands: COA.2 20 PLIP interactions: 16 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:W.185, A:K.230, A:I.387, A:I.387, A:Y.391 Hydrogen bonds: A:F.152, A:L.154, A:S.155, A:S.155, A:G.160, A:S.161, A:T.187, A:T.187, A:G.393, A:T.394, A:T.394, B:R.297, B:I.366, B:G.369 Salt bridges: B:R.297 FAD.3: 29 residues within 4Å: Chain A: Y.293, R.297, A.299, F.300, L.304, L.307, Q.365, I.366, L.367, G.368, G.369 Chain B: F.152, L.154, S.155, G.160, S.161, W.185, T.187, K.230, I.387, I.390, Y.391, G.393, T.394, E.396, I.397, L.400 Chain D: Q.308 Ligands: COA.4 20 PLIP interactions: 4 interactions with chain A, 16 interactions with chain B Hydrogen bonds: A:R.297, A:I.366, A:G.369, B:F.152, B:L.154, B:S.155, B:S.155, B:G.160, B:S.161, B:T.187, B:T.187, B:G.393, B:T.394, B:T.394 Salt bridges: A:R.297 Hydrophobic interactions: B:W.185, B:K.230, B:I.387, B:I.387, B:Y.391 FAD.5: 27 residues within 4Å: Chain A: Q.308 Chain C: F.152, L.154, S.155, G.160, S.161, W.185, T.187, K.230, I.387, I.390, Y.391, G.393, T.394, E.396, I.397, L.400 Chain D: Y.293, R.297, F.300, L.304, L.307, Q.365, I.366, G.368, G.369 Ligands: COA.6 19 PLIP interactions: 14 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:W.185, C:K.230, C:I.387, C:I.387, C:Y.391 Hydrogen bonds: C:F.152, C:L.154, C:S.155, C:S.155, C:G.160, C:S.161, C:T.187, C:G.393, C:T.394, D:Y.293, D:R.297, D:I.366, D:G.369 Salt bridges: D:R.297 FAD.7: 27 residues within 4Å: Chain B: Q.308 Chain C: Y.293, R.297, F.300, L.304, L.307, Q.365, I.366, G.368, G.369 Chain D: F.152, L.154, S.155, G.160, S.161, W.185, T.187, K.230, I.387, I.390, Y.391, G.393, T.394, E.396, I.397, L.400 Ligands: COA.8 19 PLIP interactions: 5 interactions with chain C, 14 interactions with chain D Hydrogen bonds: C:Y.293, C:R.297, C:I.366, C:G.369, D:F.152, D:L.154, D:S.155, D:S.155, D:G.160, D:S.161, D:T.187, D:G.393, D:T.394 Salt bridges: C:R.297 Hydrophobic interactions: D:W.185, D:K.230, D:I.387, D:I.387, D:Y.391

4 x COA: COENZYME A(Non-covalent)

COA.2: 22 residues within 4Å: Chain A: F.152, S.155, G.160, S.161, D.162, A.163, N.207, F.261, K.262, M.265, Q.266, L.268, D.269, R.272, I.342, Y.391, E.392, G.393, I.397, V.401 Chain B: F.300 Ligands: FAD.1 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.268, B:F.300 Hydrogen bonds: A:S.161, A:S.161, A:D.162, A:A.163, A:N.207, A:N.207, A:D.269, A:R.272, A:G.393 COA.4: 22 residues within 4Å: Chain A: F.300 Chain B: F.152, S.155, G.160, S.161, D.162, A.163, N.207, F.261, K.262, M.265, Q.266, L.268, D.269, R.272, I.342, Y.391, E.392, G.393, I.397, V.401 Ligands: FAD.3 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.268, A:F.300 Hydrogen bonds: B:S.161, B:S.161, B:D.162, B:A.163, B:N.207, B:N.207, B:D.269, B:R.272, B:G.393 COA.6: 22 residues within 4Å: Chain C: F.152, S.155, G.160, S.161, D.162, A.163, N.207, F.261, K.262, M.265, Q.266, L.268, D.269, R.272, I.342, Y.391, E.392, G.393, I.397, V.401 Chain D: F.300 Ligands: FAD.5 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.268, D:F.300 Hydrogen bonds: C:S.161, C:S.161, C:A.163, C:N.207, C:N.207, C:D.269, C:R.272, C:G.393 COA.8: 22 residues within 4Å: Chain C: F.300 Chain D: F.152, S.155, G.160, S.161, D.162, A.163, N.207, F.261, K.262, M.265, Q.266, L.268, D.269, R.272, I.342, Y.391, E.392, G.393, I.397, V.401 Ligands: FAD.7 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.268, C:F.300 Hydrogen bonds: D:S.161, D:S.161, D:A.163, D:N.207, D:N.207, D:D.269, D:R.272, D:G.393

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Z. et al., High-Resolution Structural Proteomics of Mitochondria Using the 'Build and Retrieve' Methodology. Mol.Cell Proteomics (2023)

Release Date

2024-02-21

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