SMTL ID : 1udy.1

Medium-Chain Acyl-CoA Dehydrogenase with 3-Thiaoctanoyl-CoA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 28 residues within 4Å: Chain A: Y.133, V.135, T.136, G.141, S.142, W.166, I.167, T.168, I.371, I.374, Y.375, E.376, T.378, Q.380, I.384 Chain B: R.281, T.283, F.284, L.288, H.291, I.294, Q.349, V.350, G.352, G.353, F.356 Chain D: Q.292 Ligands: CS8.2 24 PLIP interactions: 7 interactions with chain B, 16 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: B:F.356, A:W.166, A:I.371 Hydrogen bonds: B:Q.349, B:Q.349, B:G.353, A:Y.133, A:V.135, A:T.136, A:T.136, A:G.141, A:S.142, A:S.142, A:T.168, A:T.168, A:I.374, A:E.376, A:T.378, A:T.378, D:Q.292 Water bridges: B:N.354, A:G.377 Salt bridges: B:R.281, B:R.281 FAD.3: 28 residues within 4Å: Chain A: R.281, T.283, F.284, L.288, H.291, I.294, Q.349, V.350, F.351, G.352, G.353, F.356 Chain B: Y.133, V.135, T.136, G.141, S.142, W.166, I.167, T.168, I.371, Y.375, E.376, T.378, Q.380, I.381 Chain C: Q.292 Ligands: CS8.4 23 PLIP interactions: 7 interactions with chain A, 15 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: A:F.356, B:W.166, B:I.371 Hydrogen bonds: A:T.283, A:Q.349, A:G.353, B:Y.133, B:V.135, B:T.136, B:T.136, B:S.142, B:S.142, B:T.168, B:T.168, B:I.374, B:E.376, B:T.378, B:T.378, C:Q.292 Water bridges: A:N.354 Salt bridges: A:R.281, A:R.281 pi-Stacking: B:Y.375 FAD.5: 30 residues within 4Å: Chain B: Q.292 Chain C: Y.133, V.135, T.136, G.141, S.142, W.166, I.167, T.168, N.214, I.371, I.374, Y.375, E.376, T.378, Q.380, I.381, I.384 Chain D: R.281, T.283, F.284, L.288, H.291, I.294, Q.349, V.350, F.351, G.352, G.353 Ligands: CS8.6 25 PLIP interactions: 17 interactions with chain C, 7 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: C:W.166, C:I.371 Hydrogen bonds: C:Y.133, C:V.135, C:T.136, C:T.136, C:S.142, C:S.142, C:T.168, C:T.168, C:I.374, C:E.376, C:T.378, C:T.378, C:Q.380, D:Q.349, D:Q.349, D:G.353, B:Q.292 Water bridges: C:G.377, D:N.354 pi-Stacking: C:Y.375, D:H.291 Salt bridges: D:R.281, D:R.281 FAD.7: 28 residues within 4Å: Chain A: Q.292 Chain C: R.281, T.283, F.284, L.288, H.291, I.294, Q.349, V.350, F.351, G.352, G.353 Chain D: Y.133, V.135, T.136, G.141, S.142, W.166, I.167, T.168, N.214, I.371, Y.375, E.376, T.378, Q.380, I.384 Ligands: CS8.8 22 PLIP interactions: 13 interactions with chain D, 8 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: D:W.166, D:I.371 Hydrogen bonds: D:Y.133, D:V.135, D:T.136, D:T.136, D:S.142, D:S.142, D:T.168, D:E.376, D:T.378, D:Q.380, C:T.283, C:Q.349, C:Q.349, C:G.353, A:Q.292 pi-Stacking: D:Y.375, C:H.291 Water bridges: C:R.281 Salt bridges: C:R.281, C:R.281

4 x CS8: 3-THIAOCTANOYL-COENZYME A(Non-covalent)

CS8.2: 25 residues within 4Å: Chain A: T.96, E.99, L.103, Y.133, T.136, G.141, S.142, V.144, S.191, F.245, M.249, F.252, D.253, T.255, R.256, V.259, R.324, T.326, Y.375, E.376, G.377, I.381, I.385, R.388 Ligands: FAD.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:E.99, A:L.103, A:V.259, A:I.381, A:I.385 Hydrogen bonds: A:S.142, A:V.144, A:S.191, A:D.253, A:R.256, A:R.324, A:E.376, A:R.388, A:R.388 Water bridges: A:G.141, A:R.256 CS8.4: 26 residues within 4Å: Chain A: F.284 Chain B: T.96, E.99, A.100, L.103, Y.133, T.136, G.141, S.142, V.144, S.191, F.245, M.249, G.250, F.252, D.253, V.259, R.324, T.326, Y.375, E.376, G.377, I.381, I.385, R.388 Ligands: FAD.3 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:T.96, B:F.252, B:V.259, B:I.381 Hydrogen bonds: B:S.142, B:S.191, B:D.253, B:R.324, B:T.326, B:E.376, B:G.377, B:R.388 Salt bridges: B:R.388 CS8.6: 28 residues within 4Å: Chain C: T.96, E.99, A.100, L.103, Y.133, T.136, G.141, S.142, V.144, A.145, T.168, S.191, F.245, M.249, F.252, D.253, R.256, V.259, R.324, T.326, Y.375, E.376, G.377, I.381, I.385, R.388 Chain D: F.284 Ligands: FAD.5 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:E.99, C:L.103, C:V.144, C:V.259, C:E.376, C:I.385, D:F.284 Hydrogen bonds: C:S.142, C:V.144, C:S.191, C:D.253, C:R.256, C:R.324, C:T.326, C:E.376, C:R.388, C:R.388 CS8.8: 25 residues within 4Å: Chain D: T.96, E.99, A.100, L.103, Y.133, G.141, S.142, V.144, A.145, T.168, S.191, F.245, M.249, F.252, D.253, R.256, R.324, T.326, Y.375, E.376, G.377, I.381, I.385, R.388 Ligands: FAD.7 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:T.96, D:E.99, D:A.100, D:L.103, D:V.144, D:I.381, D:I.385 Hydrogen bonds: D:G.141, D:S.142, D:V.144, D:S.191, D:D.253, D:R.256, D:R.256, D:R.324, D:E.376, D:R.388, D:R.388 Water bridges: D:D.253 pi-Cation interactions: D:R.324

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Satoh, A. et al., Structure of the transition state analog of medium-chain acyl-CoA dehydrogenase. Crystallographic and molecular orbital studies on the charge-transfer complex of medium-chain acyl-CoA dehydrogenase with 3-thiaoctanoyl-CoA. J.BIOCHEM.(TOKYO) (2003)

Release Date

2003-12-09

Peptides

Acyl-CoA dehydrogenase, medium-chain specific: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Acyl-CoA dehydrogenase, medium-chain specific