SMTL ID : 2vig.1 (1 other biounit)

Crystal structure of human short-chain acyl CoA dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 29 residues within 4Å: Chain A: F.124, L.126, S.127, N.131, G.132, S.133, W.157, I.158, T.159, K.202, T.210, I.359, I.362, Y.363, E.364, T.366, E.368, I.369, L.372 Chain B: R.269, F.272, L.276, L.279, I.282, Q.337, I.338, G.340, G.341 Chain C: Q.280 29 PLIP interactions: 19 interactions with chain A, 1 interactions with chain C, 9 interactions with chain B Hydrophobic interactions: A:W.157, A:W.157, A:K.202, A:T.210, A:I.359, A:Y.363 Hydrogen bonds: A:F.124, A:L.126, A:S.127, A:S.133, A:S.133, A:T.159, A:E.364, A:T.366, A:E.368, C:Q.280, B:Q.337, B:G.341 Water bridges: A:F.124, A:D.134, A:G.365, A:G.365, B:R.269, B:R.269, B:R.269, B:M.342, B:M.342 Salt bridges: B:R.269, B:R.269 FAD.3: 30 residues within 4Å: Chain A: R.269, F.272, L.276, L.279, I.282, Q.337, I.338, G.340, G.341 Chain B: F.124, L.126, S.127, N.131, G.132, S.133, W.157, I.158, T.159, K.202, T.210, I.359, I.362, Y.363, E.364, T.366, E.368, I.369, L.372 Chain D: Q.280 Ligands: COS.4 26 PLIP interactions: 1 interactions with chain D, 7 interactions with chain A, 18 interactions with chain B Hydrogen bonds: D:Q.280, A:Q.337, A:G.341, B:F.124, B:L.126, B:S.127, B:S.133, B:S.133, B:T.159, B:T.159, B:E.364, B:T.366, B:T.366 Water bridges: A:R.269, A:M.342, A:M.342, B:D.134, B:W.157 Salt bridges: A:R.269, A:R.269 Hydrophobic interactions: B:W.157, B:W.157, B:K.202, B:T.210, B:I.359, B:Y.363 FAD.6: 31 residues within 4Å: Chain A: Q.280 Chain C: F.124, A.125, L.126, S.127, N.131, G.132, S.133, W.157, I.158, T.159, K.202, T.210, I.359, I.362, Y.363, E.364, T.366, E.368, I.369, L.372 Chain D: R.269, F.272, L.276, L.279, I.282, Q.337, I.338, G.340, G.341 Ligands: COS.7 28 PLIP interactions: 20 interactions with chain C, 7 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: C:W.157, C:W.157, C:K.202, C:T.210, C:I.359, C:Y.363 Hydrogen bonds: C:F.124, C:L.126, C:S.127, C:G.132, C:S.133, C:S.133, C:T.159, C:T.159, C:E.364, C:T.366, C:T.366, D:Q.337, D:G.341, A:Q.280 Water bridges: C:D.134, C:W.157, C:T.366, D:R.269, D:M.342, D:M.342 Salt bridges: D:R.269, D:R.269 FAD.8: 32 residues within 4Å: Chain B: Q.280 Chain C: R.269, F.272, L.276, L.279, V.281, Q.337, I.338, G.340, G.341 Chain D: F.124, A.125, L.126, S.127, N.131, G.132, S.133, W.157, I.158, T.159, K.202, I.205, T.210, I.359, I.362, Y.363, E.364, T.366, E.368, I.369, L.372 Ligands: COS.9 29 PLIP interactions: 22 interactions with chain D, 6 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: D:W.157, D:W.157, D:K.202, D:I.205, D:T.210, D:I.359, D:Y.363 Hydrogen bonds: D:F.124, D:L.126, D:S.127, D:S.127, D:G.132, D:S.133, D:S.133, D:T.159, D:E.364, D:T.366, D:E.368, C:Q.337, C:G.341, B:Q.280 Water bridges: D:F.124, D:N.131, D:D.134, D:T.366, C:R.269, C:M.342 Salt bridges: C:R.269, C:R.269

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

EDO.2: 5 residues within 4Å: Chain A: E.294, R.297, L.298, W.301 Chain C: R.302 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.302, A:R.297 EDO.5: 6 residues within 4Å: Chain B: I.28, Q.31, L.37, P.39, A.40, Q.42 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.31, B:F.38, B:Q.42 Water bridges: B:A.41 EDO.10: 4 residues within 4Å: Chain D: I.28, L.37, P.39, Q.42 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.42 Water bridges: D:A.41 EDO.11: 4 residues within 4Å: Chain B: R.302 Chain D: E.294, R.297, L.298 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:R.302, D:E.294, D:R.297

3 x COS: COENZYME A PERSULFIDE(Non-covalent)

COS.4: 17 residues within 4Å: Chain A: F.272 Chain B: F.124, G.132, S.133, A.135, F.233, M.237, Q.238, L.240, D.241, R.244, I.314, E.364, G.365, I.369, V.373 Ligands: FAD.3 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.135, B:F.233, A:F.272 Hydrogen bonds: B:G.132, B:S.133, B:Q.238, B:D.241, B:R.244, B:G.365 COS.7: 10 residues within 4Å: Chain C: F.124, S.127, G.132, S.133, L.240, R.244, E.364, G.365, I.369 Ligands: FAD.6 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.132, C:S.133, C:R.244 Water bridges: C:T.366 COS.9: 11 residues within 4Å: Chain D: F.124, L.126, S.127, G.132, S.133, L.240, R.244, E.364, G.365, I.369 Ligands: FAD.8 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.369 Hydrogen bonds: D:G.132, D:R.244, D:G.365

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pike, A.C.W. et al., Crystal Structure of Human Short-Chain Acyl Coa Dehydrogenase. To be Published

Release Date

2007-12-25

Peptides

SHORT-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE,: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

SHORT-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE,

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