SMTL ID : 1rx0.1

Crystal structure of isobutyryl-CoA dehydrogenase complexed with substrate/ligand.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-tetramer

Ligands

11 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 3 residues within 4Å: Chain A: P.15, Q.27, F.31 No protein-ligand interaction detected (PLIP) EDO.2: 3 residues within 4Å: Chain A: K.156, V.233, R.236 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.156, A:K.156, A:R.236, A:R.236 EDO.5: 4 residues within 4Å: Chain B: F.169, E.211 Chain D: Y.354, L.357 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.169 EDO.6: 5 residues within 4Å: Chain B: L.138, A.148, I.193, F.244, A.247 No protein-ligand interaction detected (PLIP) EDO.7: 6 residues within 4Å: Chain B: P.15, Q.27, F.31, A.89, T.92, H.267 No protein-ligand interaction detected (PLIP) EDO.8: 4 residues within 4Å: Chain B: H.276, R.280, Y.354, Y.360 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.360 Water bridges: B:H.276, B:R.280, B:Y.354 EDO.12: 4 residues within 4Å: Chain C: P.15, Q.27, F.31, E.88 1 PLIP interactions: 1 interactions with chain C Water bridges: C:A.89 EDO.13: 5 residues within 4Å: Chain C: R.249, L.318, E.321, R.322, A.325 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.249, C:E.321 Water bridges: C:N.252, C:V.326 EDO.14: 5 residues within 4Å: Chain A: P.141 Chain C: H.276, R.280, Y.354, Y.360 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.280 Water bridges: C:H.276 EDO.18: 5 residues within 4Å: Chain D: P.15, F.31, E.88, T.92, H.267 No protein-ligand interaction detected (PLIP) EDO.19: 2 residues within 4Å: Chain D: F.283, G.284 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.146, B:D.146

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

FAD.3: 30 residues within 4Å: Chain A: Y.136, L.138, T.139, G.144, S.145, A.168, F.169, I.170, S.171, K.213, W.216, V.371, I.374, L.375, S.378, E.380, I.384 Chain B: Q.291 Chain C: R.280, Q.282, F.283, L.287, N.290, L.293, Q.349, M.350, G.352, G.353, Y.354, Y.356 27 PLIP interactions: 18 interactions with chain A, 8 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: A:F.169, A:K.213, A:W.216, A:W.216, A:V.371, A:L.375, A:L.375, C:Y.356 Hydrogen bonds: A:Y.136, A:L.138, A:T.139, A:T.139, A:S.145, A:S.145, A:S.171, A:S.378, A:S.378, C:N.290, C:N.290, C:Q.349, C:G.353, B:Q.291 Water bridges: A:G.377, A:S.378, C:R.280 Salt bridges: C:R.280, C:R.280 FAD.9: 31 residues within 4Å: Chain A: Q.291 Chain B: Y.136, L.138, T.139, G.144, S.145, A.168, F.169, I.170, S.171, K.213, W.216, V.371, I.374, L.375, S.378, E.380, I.384 Chain D: R.280, Q.282, F.283, L.287, N.290, L.293, Q.349, M.350, G.352, G.353, Y.354, Y.356 Ligands: ACY.22 27 PLIP interactions: 8 interactions with chain D, 18 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: D:Y.356, B:F.169, B:K.213, B:W.216, B:W.216, B:V.371, B:L.375 Hydrogen bonds: D:N.290, D:Q.349, D:G.353, B:Y.136, B:L.138, B:T.139, B:T.139, B:S.145, B:S.145, B:S.171, B:S.378, B:S.378, B:E.380, A:Q.291 Water bridges: D:R.280, D:N.290, B:G.144, B:G.377 Salt bridges: D:R.280, D:R.280 FAD.15: 32 residues within 4Å: Chain A: R.280, Q.282, F.283, L.287, N.290, L.293, Q.349, M.350, G.352, G.353, Y.354, Y.356 Chain C: Y.136, C.137, L.138, T.139, G.144, S.145, A.168, F.169, I.170, S.171, K.213, W.216, V.371, I.374, L.375, S.378, E.380, I.384 Chain D: Q.291 Ligands: 2MC.16 26 PLIP interactions: 17 interactions with chain C, 8 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: C:F.169, C:F.169, C:K.213, C:W.216, C:W.216, C:V.371, C:L.375, A:Y.356 Hydrogen bonds: C:Y.136, C:L.138, C:T.139, C:T.139, C:S.145, C:S.145, C:S.171, C:S.378, C:S.378, A:N.290, A:N.290, A:Q.349, A:G.353, D:Q.291 Water bridges: C:S.378, A:R.280 Salt bridges: A:R.280, A:R.280 FAD.20: 32 residues within 4Å: Chain B: R.280, Q.282, F.283, L.287, N.290, L.293, Q.349, M.350, G.352, G.353, Y.354, Y.356 Chain C: Q.291 Chain D: Y.136, C.137, L.138, T.139, G.144, S.145, A.168, F.169, I.170, S.171, W.216, V.371, I.374, L.375, S.378, E.380, I.384 Ligands: ACY.10, 2MC.21 24 PLIP interactions: 1 interactions with chain C, 16 interactions with chain D, 7 interactions with chain B Hydrogen bonds: C:Q.291, D:Y.136, D:L.138, D:T.139, D:T.139, D:S.145, D:S.145, D:S.171, D:S.378, D:S.378, D:E.380, B:N.290, B:Q.349, B:G.353 Hydrophobic interactions: D:F.169, D:F.169, D:W.216, D:W.216, D:V.371, D:L.375, B:Y.356 Water bridges: B:R.280 Salt bridges: B:R.280, B:R.280

7 x ACY: ACETIC ACID(Non-functional Binders)

ACY.4: 4 residues within 4Å: Chain A: Y.68, L.78, R.80, W.109 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.68 Water bridges: A:R.80, A:R.80 Salt bridges: A:R.80 ACY.10: 5 residues within 4Å: Chain B: F.283, N.290 Chain C: Q.291 Chain D: R.388 Ligands: FAD.20 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:Q.291 Hydrophobic interactions: B:F.283 Water bridges: B:N.290 ACY.11: 3 residues within 4Å: Chain B: Q.61, L.62, G.63 No protein-ligand interaction detected (PLIP) ACY.17: 3 residues within 4Å: Chain C: G.142, S.149, L.151 2 PLIP interactions: 2 interactions with chain C Water bridges: C:S.149, C:L.151 ACY.22: 4 residues within 4Å: Chain B: I.384, R.388 Chain D: F.283 Ligands: FAD.9 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.291 ACY.23: 4 residues within 4Å: Chain D: F.26, L.62, F.64, L.78 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.26 ACY.24: 3 residues within 4Å: Chain D: L.81, R.312, V.316 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:R.312, D:V.316

2 x 2MC: METHACRYLYL-COENZYME A(Non-covalent)

2MC.16: 23 residues within 4Å: Chain A: F.283 Chain C: I.103, M.106, Y.136, T.139, G.144, S.145, A.147, A.148, P.190, F.244, V.248, L.251, N.252, R.255, V.326, L.375, E.376, G.377, V.381, L.385, R.388 Ligands: FAD.15 22 PLIP interactions: 21 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:I.103, C:I.103, C:A.147, C:L.375, C:E.376, C:V.381, C:L.385, A:F.283 Hydrogen bonds: C:S.145, C:A.147, C:N.252, C:N.252, C:R.255, C:R.255, C:E.376, C:G.377, C:R.388 Water bridges: C:T.139, C:G.144, C:A.148 Salt bridges: C:K.191, C:R.388 2MC.21: 23 residues within 4Å: Chain B: F.283 Chain D: I.103, Y.136, L.138, T.139, G.144, S.145, A.147, A.148, P.190, F.244, V.248, L.251, N.252, R.255, V.326, L.375, E.376, G.377, V.381, L.385, R.388 Ligands: FAD.20 19 PLIP interactions: 1 interactions with chain B, 18 interactions with chain D Hydrophobic interactions: B:F.283, D:A.147, D:L.375, D:E.376, D:V.381, D:L.385 Hydrogen bonds: D:S.145, D:A.147, D:N.252, D:N.252, D:R.255, D:R.255, D:E.376, D:G.377 Water bridges: D:T.139, D:G.144, D:A.148 Salt bridges: D:R.388, D:R.388

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Battaile, K.P. et al., Structures of Isobutyryl-CoA Dehydrogenase and Enzyme-Product Complex: COMPARISON WITH ISOVALERYL- AND SHORT-CHAIN ACYL-COA DEHYDROGENASES. J.Biol.Chem. (2004)

Release Date

2004-04-20

Peptides

Acyl-CoA dehydrogenase family member 8, mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Acyl-CoA dehydrogenase family member 8, mitochondrial