SMTL ID : 2jif.1

Structure of human short-branched chain acyl-CoA dehydrogenase (ACADSB)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 30 residues within 4Å: Chain A: F.146, L.148, S.149, G.154, S.155, W.179, I.180, S.181, K.224, T.232, I.381, I.384, Y.385, E.386, A.388, N.390, I.391, N.394 Chain B: Q.302 Chain C: R.291, Q.293, F.294, L.298, F.301, L.304, E.359, W.360, G.362, G.363 Ligands: COS.2 29 PLIP interactions: 9 interactions with chain C, 19 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:E.359, C:G.363, A:F.146, A:L.148, A:S.149, A:S.149, A:S.155, A:S.155, A:S.181, A:E.386, A:N.390, A:N.390, A:N.394, B:Q.302 Water bridges: C:R.291, C:R.291, C:V.364, A:S.149, A:G.154, A:W.179 Salt bridges: C:R.291, C:R.291 pi-Stacking: C:F.301, C:F.301, A:Y.385 Hydrophobic interactions: A:W.179, A:W.179, A:K.224, A:T.232 FAD.6: 30 residues within 4Å: Chain A: Q.302 Chain B: F.146, L.148, S.149, G.154, S.155, W.179, I.180, S.181, K.224, T.232, I.381, I.384, Y.385, E.386, A.388, N.390, I.391, N.394 Chain D: R.291, Q.293, F.294, L.298, F.301, L.304, E.359, W.360, G.362, G.363 Ligands: COS.7 32 PLIP interactions: 13 interactions with chain D, 18 interactions with chain B, 1 interactions with chain A Hydrogen bonds: D:Q.293, D:E.359, D:G.363, B:F.146, B:L.148, B:S.149, B:S.149, B:S.155, B:S.155, B:S.181, B:E.386, B:N.390, B:N.394, A:Q.302 Water bridges: D:Y.287, D:R.291, D:R.291, D:R.291, D:E.359, D:V.364, B:W.179, B:N.390 Salt bridges: D:R.291, D:R.291 pi-Stacking: D:F.301, D:F.301, B:Y.385 Hydrophobic interactions: B:W.179, B:K.224, B:T.232, B:I.381, B:Y.385 FAD.12: 30 residues within 4Å: Chain A: R.291, Q.293, F.294, L.298, F.301, L.304, E.359, W.360, G.362, G.363 Chain C: F.146, L.148, S.149, G.154, S.155, W.179, I.180, S.181, K.224, T.232, I.381, I.384, Y.385, E.386, A.388, N.390, I.391, N.394 Chain D: Q.302 Ligands: COS.13 29 PLIP interactions: 15 interactions with chain C, 13 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: C:W.179, C:K.224, C:T.232 Hydrogen bonds: C:F.146, C:L.148, C:S.149, C:S.149, C:S.155, C:S.155, C:S.181, C:E.386, C:N.390, C:N.390, C:N.394, A:Q.293, A:E.359, A:G.363, D:Q.302 pi-Stacking: C:Y.385, A:F.301, A:F.301 Water bridges: A:R.291, A:R.291, A:R.291, A:R.291, A:Q.307, A:V.364 Salt bridges: A:R.291, A:R.291 FAD.17: 31 residues within 4Å: Chain B: R.291, Q.293, F.294, L.298, F.301, L.304, E.359, W.360, G.362, G.363 Chain C: Q.302 Chain D: F.146, L.148, S.149, G.154, S.155, W.179, I.180, S.181, K.224, T.232, I.381, I.384, Y.385, E.386, A.388, N.390, I.391, N.394 Ligands: COS.18, EDO.21 31 PLIP interactions: 18 interactions with chain D, 1 interactions with chain C, 12 interactions with chain B Hydrophobic interactions: D:W.179, D:W.179, D:K.224, D:T.232, D:I.381 Hydrogen bonds: D:F.146, D:L.148, D:S.149, D:S.149, D:S.155, D:S.155, D:S.181, D:E.386, D:N.390, D:N.390, D:N.394, C:Q.302, B:Q.293, B:E.359, B:G.363 Water bridges: D:W.179, B:R.291, B:R.291, B:R.291, B:R.291, B:Q.307, B:V.364 pi-Stacking: D:Y.385, B:F.301 Salt bridges: B:R.291, B:R.291

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

COS.2: 18 residues within 4Å: Chain A: S.155, S.157, F.158, Y.201, K.202, Y.255, I.259, L.262, N.263, R.266, I.336, Y.385, E.386, G.387, I.391, K.398 Chain C: F.294 Ligands: FAD.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.259 Hydrogen bonds: A:S.155, A:S.157, A:S.157, A:Y.255, A:N.263, A:N.263, A:R.266, A:R.266, A:G.387 Water bridges: A:D.156 Salt bridges: A:K.202 COS.7: 16 residues within 4Å: Chain B: S.155, S.157, F.158, Y.201, Y.255, I.259, L.262, N.263, R.266, I.336, Y.385, E.386, G.387, I.391 Chain D: F.294 Ligands: FAD.6 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.259 Hydrogen bonds: B:S.155, B:S.157, B:S.157, B:Y.201, B:Y.255, B:Y.255, B:N.263, B:N.263, B:R.266, B:R.266, B:G.387 Water bridges: B:T.395 Salt bridges: B:K.202 COS.13: 17 residues within 4Å: Chain A: F.294 Chain C: S.155, S.157, F.158, Y.201, K.202, Y.255, I.259, L.262, N.263, R.266, I.336, Y.385, E.386, G.387, I.391 Ligands: FAD.12 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:I.259 Hydrogen bonds: C:S.155, C:S.157, C:S.157, C:Y.201, C:Y.201, C:Y.255, C:N.263, C:N.263, C:R.266, C:G.387 Water bridges: C:K.202, C:R.266, C:T.395, C:K.398, C:K.398 Salt bridges: C:K.202 COS.18: 20 residues within 4Å: Chain B: F.294 Chain D: S.155, S.157, F.158, Y.201, K.202, Y.255, K.256, I.259, L.262, N.263, R.266, I.336, Y.385, E.386, G.387, I.391, K.398 Ligands: FAD.17, EDO.21 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:F.158, D:I.259 Hydrogen bonds: D:S.155, D:S.157, D:S.157, D:Y.255, D:N.263, D:N.263, D:R.266, D:R.266 Water bridges: D:K.202, D:K.256, D:G.260 Salt bridges: D:K.202

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

EDO.3: 3 residues within 4Å: Chain A: V.103, P.371, Y.375 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.103 Water bridges: A:Y.375 EDO.8: 6 residues within 4Å: Chain B: R.228, K.368, R.377 Chain D: R.228, K.368, R.377 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:R.228, B:R.228, B:K.368 Water bridges: D:K.368, D:R.377, B:R.377 EDO.14: 4 residues within 4Å: Chain C: A.49, V.103, P.371, Y.375 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.103, C:Y.375 EDO.19: 5 residues within 4Å: Chain D: Q.130, Y.134, L.208, A.245, N.246 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.130, D:Y.134, D:N.246 EDO.20: 6 residues within 4Å: Chain D: V.209, D.210, T.213, K.241, P.243, N.246 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.210, D:T.213 EDO.21: 5 residues within 4Å: Chain B: F.294 Chain D: I.391, N.394 Ligands: FAD.17, COS.18 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.394 EDO.22: 4 residues within 4Å: Chain D: V.52, V.103, P.371, Y.375 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.103

10 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: V.79, D.80, Y.83, R.123 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: F.110, S.182, H.185, S.231 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: V.79, D.80, Y.83, R.123 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: F.110, S.182, H.185, S.231 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: Y.345 Chain B: Q.314, Y.345 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain C: D.80, Y.83, R.123 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain C: F.110, S.182, A.229, S.230, S.231 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain D: V.79, D.80, Y.83, R.123 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain D: F.110, S.182, H.185, S.231 Ligand excluded by PLIP CL.25: 4 residues within 4Å: Chain C: Q.314, Y.345 Chain D: Q.314, Y.345 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2007-04-03

Peptides

SHORT/BRANCHED CHAIN SPECIFIC ACYL-COA DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

SHORT/BRANCHED CHAIN SPECIFIC ACYL-COA DEHYDROGENASE