SMTL ID : 2vig.2 (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: 30 residues within 4Å: Chain A: 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 B: R.269, F.272, L.276, L.279, V.281, Q.337, I.338, G.340, G.341 Chain C: Q.280 28 PLIP interactions: 20 interactions with chain A, 7 interactions with chain B, 1 interactions with chain C 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:G.132, A:S.133, A:S.133, A:T.159, A:E.364, A:T.366, A:E.368, B:Q.337, B:G.341, C:Q.280 Water bridges: A:D.134, A:W.157, A:G.365, A:G.365, B:R.269, B:M.342, B:M.342 Salt bridges: B:R.269, B:R.269 FAD.5: 30 residues within 4Å: Chain A: R.269, F.272, L.276, L.279, V.281, 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.6 26 PLIP interactions: 18 interactions with chain B, 7 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: B:W.157, B:W.157, B:K.202, B:T.210, B:Y.363 Hydrogen bonds: B:F.124, B:L.126, B:S.127, B:G.132, B:S.133, B:S.133, B:T.159, B:T.159, B:E.364, B:T.366, B:T.366, A:Q.337, A:G.341, D:Q.280 Water bridges: B:D.134, B:W.157, A:R.269, A:M.342, A:M.342 Salt bridges: A:R.269, A:R.269 FAD.10: 29 residues within 4Å: Chain A: Q.280 Chain C: 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, L.372 Chain D: R.269, F.272, L.276, L.279, I.282, Q.337, I.338, G.340, G.341 Ligands: COS.11 27 PLIP interactions: 1 interactions with chain A, 19 interactions with chain C, 7 interactions with chain D Hydrogen bonds: A:Q.280, 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 Hydrophobic interactions: C:W.157, C:W.157, C:K.202, C:T.210 Water bridges: C:F.124, C:N.131, C:D.134, D:R.269, D:M.342, D:M.342 pi-Stacking: C:Y.363 Salt bridges: D:R.269, D:R.269 FAD.12: 29 residues within 4Å: Chain B: Q.280 Chain C: R.269, F.272, L.276, L.279, I.282, 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, T.210, I.359, I.362, Y.363, E.364, T.366, E.368, L.372 31 PLIP interactions: 23 interactions with chain D, 7 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: D:W.157, D:W.157, D:K.202, D:T.210, D:I.359, D:Y.363 Hydrogen bonds: D:F.124, D:L.126, D:S.127, D:S.127, 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:G.132, D:G.132, D:W.157, D:G.365, D:G.365, D:T.366, C:Y.265, C:R.269, C:M.342 Salt bridges: C:R.269, C:R.269

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

EDO.2: 5 residues within 4Å: Chain A: Q.31, V.32, L.37, P.39, Q.42 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.38, A:A.40, A:Q.42 Water bridges: A:A.41 EDO.3: 5 residues within 4Å: Chain A: E.294, R.297, L.298, W.301 Chain C: R.302 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:E.294, A:R.297, C:R.302 EDO.4: 6 residues within 4Å: Chain A: E.128, P.129, S.139, T.140, G.153, T.154 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.128, A:T.154 Water bridges: A:N.131, A:G.153, A:T.154 EDO.7: 4 residues within 4Å: Chain B: I.28, Q.31, P.39, Q.42 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.42 Water bridges: B:A.40, B:A.41 EDO.8: 4 residues within 4Å: Chain B: E.106, Q.107, A.110, W.111 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.111 Water bridges: B:S.104 EDO.9: 6 residues within 4Å: Chain B: E.128, P.129, S.139, T.140, G.153, T.154 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.128, B:T.154 Water bridges: B:E.128, B:S.139, B:T.154 EDO.13: 5 residues within 4Å: Chain D: I.28, Q.31, L.37, P.39, Q.42 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.31, D:F.38, D:Q.42 Water bridges: D:A.41 EDO.14: 5 residues within 4Å: Chain B: R.302 Chain D: E.294, R.297, L.298, W.301 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:E.294, D:R.297, B:R.302

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

COS.6: 11 residues within 4Å: Chain B: F.124, S.127, G.132, S.133, A.135, M.237, L.240, R.244, E.364, G.365 Ligands: FAD.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.132, B:R.244 COS.11: 19 residues within 4Å: Chain C: F.124, L.126, G.132, S.133, A.135, N.179, F.233, M.237, Q.238, L.240, D.241, R.244, I.314, Y.363, E.364, G.365, V.373 Chain D: F.272 Ligands: FAD.10 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:A.135, D:F.272 Hydrogen bonds: C:G.132, C:S.133, C:N.179, C:N.179, C:D.241, C:R.244, C: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
E

B
F

C
G

D
H

SHORT-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE,

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