SMTL ID : 2r0n.2 (1 other biounit)

The effect of a Glu370Asp mutation in Glutaryl-CoA Dehydrogenase on Proton Transfer to the Dienolate Intermediate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 29 residues within 4Å: Chain A: F.133, L.135, T.136, G.141, S.142, W.168, I.169, T.170, L.212, T.368, Y.369, E.370, G.371, T.372, D.374, F.390 Chain C: Q.286 Chain D: R.275, Q.277, F.278, L.282, N.285, I.288, D.343, M.344, G.346, G.347, I.350 Ligands: TGC.2 27 PLIP interactions: 9 interactions with chain D, 17 interactions with chain A, 1 interactions with chain C Hydrogen bonds: D:N.285, D:D.343, D:G.347, A:F.133, A:L.135, A:T.136, A:T.136, A:S.142, A:S.142, A:T.170, A:T.170, A:E.370, A:G.371, A:T.372, A:T.372, A:F.390, C:Q.286 Water bridges: D:R.275, D:R.275, D:N.348, D:N.348 Salt bridges: D:R.275, D:R.275 Hydrophobic interactions: A:W.168, A:L.212, A:Y.369 pi-Stacking: A:Y.369 FAD.3: 29 residues within 4Å: Chain B: F.133, L.135, T.136, G.141, S.142, W.168, I.169, T.170, L.212, T.368, Y.369, E.370, G.371, T.372, D.374, F.390 Chain C: R.275, Q.277, F.278, L.282, N.285, I.288, D.343, M.344, G.346, G.347, I.350 Chain D: Q.286 Ligands: TGC.4 27 PLIP interactions: 9 interactions with chain C, 17 interactions with chain B, 1 interactions with chain D Hydrogen bonds: C:N.285, C:D.343, C:G.347, B:F.133, B:L.135, B:T.136, B:T.136, B:S.142, B:S.142, B:T.170, B:T.170, B:E.370, B:G.371, B:T.372, B:T.372, B:F.390, D:Q.286 Water bridges: C:R.275, C:R.275, C:N.348, C:N.348 Salt bridges: C:R.275, C:R.275 Hydrophobic interactions: B:W.168, B:L.212, B:Y.369 pi-Stacking: B:Y.369 FAD.5: 29 residues within 4Å: Chain A: Q.286 Chain B: R.275, Q.277, F.278, L.282, N.285, I.288, D.343, M.344, G.346, G.347, I.350 Chain C: F.133, L.135, T.136, G.141, S.142, W.168, I.169, T.170, L.212, T.368, Y.369, E.370, G.371, T.372, D.374, F.390 Ligands: TGC.6 26 PLIP interactions: 9 interactions with chain B, 16 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:N.285, B:D.343, B:G.347, C:F.133, C:L.135, C:T.136, C:T.136, C:S.142, C:S.142, C:T.170, C:E.370, C:G.371, C:T.372, C:D.374, C:F.390, A:Q.286 Water bridges: B:R.275, B:R.275, B:N.348, B:N.348 Salt bridges: B:R.275, B:R.275 Hydrophobic interactions: C:W.168, C:L.212, C:Y.369 pi-Stacking: C:Y.369 FAD.7: 29 residues within 4Å: Chain A: R.275, Q.277, F.278, L.282, N.285, I.288, D.343, M.344, G.346, G.347, I.350 Chain B: Q.286 Chain D: F.133, L.135, T.136, G.141, S.142, W.168, I.169, T.170, L.212, T.368, Y.369, E.370, G.371, T.372, D.374, F.390 Ligands: TGC.8 26 PLIP interactions: 1 interactions with chain B, 16 interactions with chain D, 9 interactions with chain A Hydrogen bonds: B:Q.286, D:F.133, D:L.135, D:T.136, D:T.136, D:S.142, D:S.142, D:T.170, D:E.370, D:G.371, D:T.372, D:D.374, D:F.390, A:N.285, A:D.343, A:G.347 Hydrophobic interactions: D:W.168, D:L.212, D:Y.369 pi-Stacking: D:Y.369 Water bridges: A:R.275, A:R.275, A:N.348, A:N.348 Salt bridges: A:R.275, A:R.275

4 x TGC: 3-thiaglutaryl-CoA(Non-covalent)

TGC.2: 26 residues within 4Å: Chain A: R.94, S.95, S.98, V.99, L.103, F.133, L.135, G.141, S.142, P.144, T.170, L.239, G.240, F.243, L.246, N.247, R.250, P.320, Y.369, E.370, G.371, I.375, I.379, R.382, F.390 Ligands: FAD.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.144, A:F.243, A:F.243 Hydrogen bonds: A:S.142, A:N.247, A:R.250, A:E.370, A:E.370, A:G.371 Water bridges: A:R.382 Salt bridges: A:R.94, A:R.382 pi-Stacking: A:F.243 TGC.4: 26 residues within 4Å: Chain B: R.94, S.95, S.98, V.99, L.103, F.133, L.135, G.141, S.142, P.144, T.170, L.239, G.240, F.243, L.246, N.247, R.250, P.320, Y.369, E.370, G.371, I.375, I.379, R.382, F.390 Ligands: FAD.3 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:P.144, B:F.243, B:F.243 Hydrogen bonds: B:S.142, B:N.247, B:R.250, B:E.370, B:E.370, B:G.371 Water bridges: B:R.382 Salt bridges: B:R.94, B:R.382 pi-Stacking: B:F.243 TGC.6: 26 residues within 4Å: Chain C: R.94, S.95, S.98, V.99, L.103, F.133, L.135, G.141, S.142, P.144, T.170, L.239, G.240, F.243, L.246, N.247, R.250, P.320, Y.369, E.370, G.371, I.375, I.379, R.382, F.390 Ligands: FAD.5 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:P.144, C:F.243, C:F.243 Hydrogen bonds: C:S.142, C:N.247, C:R.250, C:E.370, C:G.371 Water bridges: C:R.382 Salt bridges: C:R.94, C:R.382 pi-Stacking: C:F.243 TGC.8: 26 residues within 4Å: Chain D: R.94, S.95, S.98, V.99, L.103, F.133, L.135, G.141, S.142, P.144, T.170, L.239, G.240, F.243, L.246, N.247, R.250, P.320, Y.369, E.370, G.371, I.375, I.379, R.382, F.390 Ligands: FAD.7 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:P.144, D:F.243, D:F.243 Hydrogen bonds: D:S.142, D:N.247, D:R.250, D:E.370, D:G.371 Water bridges: D:R.382 Salt bridges: D:R.94, D:R.382 pi-Stacking: D:F.243

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rao, K.S. et al., The effect of a Glu370Asp mutation in glutaryl-CoA dehydrogenase on proton transfer to the dienolate intermediate. Biochemistry (2007)

Release Date

2008-04-22

Peptides

Glutaryl-CoA dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Glutaryl-CoA dehydrogenase

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