SMTL ID : 3mde.1

CRYSTAL STRUCTURES OF MEDIUM CHAIN ACYL-COA DEHYDROGENASE FROM PIG LIVER MITOCHONDRIA WITH AND WITHOUT SUBSTRATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x CO8: OCTANOYL-COENZYME A(Non-covalent)

CO8.1: 25 residues within 4Å: Chain A: T.86, E.89, A.90, L.93, G.131, S.132, V.134, A.135, T.158, S.181, F.235, M.239, F.242, D.243, R.246, R.314, T.316, Y.365, E.366, G.367, I.371, I.375, R.378 Chain B: F.274 Ligands: FAD.2 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.86, A:E.89, A:V.134, A:Y.365, A:E.366, A:I.375, B:F.274 Hydrogen bonds: A:G.131, A:S.132, A:V.134, A:S.181, A:D.243, A:R.246, A:R.314, A:E.366, A:G.367, A:R.378 Water bridges: A:A.135, A:R.246, A:R.378 CO8.3: 22 residues within 4Å: Chain B: T.86, E.89, A.90, L.93, T.126, G.131, S.132, V.134, S.181, F.235, M.239, F.242, D.243, R.314, T.316, Y.365, E.366, G.367, I.371, I.375, R.378 Ligands: FAD.4 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:T.86, B:E.89, B:V.134, B:Y.365, B:E.366, B:I.375 Hydrogen bonds: B:G.131, B:S.132, B:V.134, B:S.181, B:D.243, B:R.314, B:T.316, B:E.366, B:R.378 Water bridges: B:A.135 CO8.5: 25 residues within 4Å: Chain C: T.86, E.89, A.90, L.93, G.131, S.132, V.134, A.135, T.158, S.181, F.235, M.239, F.242, D.243, R.246, R.314, T.316, Y.365, E.366, G.367, I.371, I.375, R.378 Chain D: F.274 Ligands: FAD.6 21 PLIP interactions: 20 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:T.86, C:E.89, C:V.134, C:Y.365, C:E.366, C:I.375, D:F.274 Hydrogen bonds: C:G.131, C:S.132, C:V.134, C:S.181, C:D.243, C:R.246, C:R.314, C:T.316, C:E.366, C:G.367, C:R.378 Water bridges: C:A.135, C:R.246, C:R.378 CO8.7: 22 residues within 4Å: Chain D: T.86, E.89, A.90, L.93, T.126, G.131, S.132, V.134, S.181, F.235, M.239, F.242, D.243, R.314, T.316, Y.365, E.366, G.367, I.371, I.375, R.378 Ligands: FAD.8 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:T.86, D:E.89, D:V.134, D:Y.365, D:E.366, D:I.375 Hydrogen bonds: D:G.131, D:S.132, D:V.134, D:S.181, D:D.243, D:R.314, D:E.366, D:R.378 Water bridges: D:A.135

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

FAD.2: 29 residues within 4Å: Chain A: Y.123, V.125, T.126, G.131, S.132, W.156, I.157, T.158, N.204, I.361, I.364, Y.365, E.366, T.368, Q.370, I.371, I.374 Chain B: R.271, T.273, F.274, L.278, H.281, I.284, Q.339, V.340, G.342, G.343 Chain D: Q.282 Ligands: CO8.1 28 PLIP interactions: 18 interactions with chain A, 2 interactions with chain D, 8 interactions with chain B Hydrophobic interactions: A:W.156, A:I.361, A:Y.365 Hydrogen bonds: A:Y.123, A:V.125, A:T.126, A:T.126, A:S.132, A:S.132, A:T.158, A:T.158, A:E.366, A:T.368, D:Q.282, D:Q.282, B:T.273, B:Q.339, B:G.343 Water bridges: A:Y.123, A:A.130, A:G.131, A:D.133, A:T.368, B:R.271, B:N.344 Salt bridges: B:R.271, B:R.271 pi-Stacking: B:H.281 FAD.4: 28 residues within 4Å: Chain A: R.271, T.273, F.274, L.278, H.281, I.284, Q.339, V.340, G.342, G.343 Chain B: Y.123, V.125, T.126, G.131, S.132, W.156, I.157, T.158, N.204, I.361, I.364, Y.365, E.366, T.368, Q.370, I.374 Chain C: Q.282 Ligands: CO8.3 29 PLIP interactions: 1 interactions with chain C, 18 interactions with chain B, 10 interactions with chain A Hydrogen bonds: C:Q.282, B:Y.123, B:V.125, B:T.126, B:T.126, B:S.132, B:S.132, B:T.158, B:T.158, B:E.366, B:T.368, B:T.368, B:Q.370, A:T.273, A:Q.339, A:Q.339, A:G.343 Hydrophobic interactions: B:W.156, B:I.361 Water bridges: B:G.131, B:D.133, B:T.368, A:R.271, A:R.271, A:N.344 pi-Stacking: B:Y.365, A:H.281 Salt bridges: A:R.271, A:R.271 FAD.6: 29 residues within 4Å: Chain B: Q.282 Chain C: Y.123, V.125, T.126, G.131, S.132, W.156, I.157, T.158, N.204, I.361, I.364, Y.365, E.366, T.368, Q.370, I.371, I.374 Chain D: R.271, T.273, F.274, L.278, H.281, I.284, Q.339, V.340, G.342, G.343 Ligands: CO8.5 27 PLIP interactions: 7 interactions with chain D, 18 interactions with chain C, 2 interactions with chain B Hydrogen bonds: D:Q.339, D:G.343, C:Y.123, C:V.125, C:T.126, C:T.126, C:S.132, C:S.132, C:T.158, C:E.366, C:T.368, C:T.368, B:Q.282, B:Q.282 Water bridges: D:R.271, D:N.344, C:Y.123, C:A.130, C:G.131, C:D.133, C:T.368 Salt bridges: D:R.271, D:R.271 pi-Stacking: D:H.281 Hydrophobic interactions: C:W.156, C:I.361, C:Y.365 FAD.8: 28 residues within 4Å: Chain A: Q.282 Chain C: R.271, T.273, F.274, L.278, H.281, I.284, Q.339, V.340, G.342, G.343 Chain D: Y.123, V.125, T.126, G.131, S.132, W.156, I.157, T.158, N.204, I.361, I.364, Y.365, E.366, T.368, Q.370, I.374 Ligands: CO8.7 26 PLIP interactions: 16 interactions with chain D, 1 interactions with chain A, 9 interactions with chain C Hydrophobic interactions: D:W.156, D:I.361 Hydrogen bonds: D:Y.123, D:V.125, D:T.126, D:T.126, D:S.132, D:S.132, D:T.158, D:E.366, D:T.368, D:Q.370, A:Q.282, C:Q.339, C:Q.339, C:G.343 Water bridges: D:G.131, D:D.133, D:T.368, C:R.271, C:R.271, C:N.344 pi-Stacking: D:Y.365, C:H.281 Salt bridges: C:R.271, C:R.271

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, J.J. et al., Crystal structures of medium-chain acyl-CoA dehydrogenase from pig liver mitochondria with and without substrate. Proc.Natl.Acad.Sci.USA (1993)

Release Date

1994-09-30

Peptides

MEDIUM CHAIN ACYL-COA DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

MEDIUM CHAIN ACYL-COA DEHYDROGENASE

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