SMTL ID : 2r0m.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 28 residues within 4Å: Chain A: F.133, L.135, T.136, G.141, S.142, W.168, I.169, T.170, L.212, A.365, T.368, Y.369, D.370, T.372, D.374, F.390 Chain C: Q.286 Chain D: R.275, Q.277, F.278, L.282, N.285, D.343, M.344, G.346, G.347, I.350 Ligands: 4NI.2 26 PLIP interactions: 17 interactions with chain A, 9 interactions with chain D Hydrophobic interactions: A:L.212, A:A.365, A:Y.369 Hydrogen bonds: 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:D.370, A:T.372, A:T.372, A:F.390, D:N.285, D:D.343, D:G.347 Water bridges: A:T.372, D:Y.271, D:R.275, D:R.275, D:N.348 pi-Stacking: A:Y.369 Salt bridges: D:R.275, D:R.275 FAD.3: 28 residues within 4Å: Chain B: F.133, L.135, T.136, G.141, S.142, W.168, I.169, T.170, L.212, A.365, T.368, Y.369, D.370, T.372, D.374, F.390 Chain C: R.275, Q.277, F.278, L.282, N.285, D.343, M.344, G.346, G.347, I.350 Chain D: Q.286 Ligands: 4NI.4 26 PLIP interactions: 17 interactions with chain B, 9 interactions with chain C Hydrophobic interactions: B:L.212, B:A.365, B:Y.369 Hydrogen bonds: 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:D.370, B:T.372, B:T.372, B:F.390, C:N.285, C:D.343, C:G.347 Water bridges: B:T.372, C:Y.271, C:R.275, C:R.275, C:N.348 pi-Stacking: B:Y.369 Salt bridges: C:R.275, C:R.275 FAD.5: 28 residues within 4Å: Chain A: Q.286 Chain B: R.275, Q.277, F.278, L.282, N.285, 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, A.365, T.368, Y.369, D.370, T.372, D.374, F.390 Ligands: 4NI.6 25 PLIP interactions: 16 interactions with chain C, 9 interactions with chain B Hydrophobic interactions: C:L.212, C:A.365, C:Y.369 Hydrogen bonds: C:F.133, C:L.135, C:T.136, C:T.136, C:S.142, C:S.142, C:T.170, C:D.370, C:T.372, C:D.374, C:F.390, B:N.285, B:D.343, B:D.343, B:G.347 Water bridges: C:T.372, B:R.275, B:R.275, B:N.348 pi-Stacking: C:Y.369 Salt bridges: B:R.275, B:R.275 FAD.7: 28 residues within 4Å: Chain A: R.275, Q.277, F.278, L.282, N.285, 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, A.365, T.368, Y.369, D.370, T.372, D.374, F.390 Ligands: 4NI.8 25 PLIP interactions: 16 interactions with chain D, 9 interactions with chain A Hydrophobic interactions: D:L.212, D:A.365, D:Y.369 Hydrogen bonds: D:F.133, D:L.135, D:T.136, D:T.136, D:S.142, D:S.142, D:T.170, D:D.370, D:T.372, D:D.374, D:F.390, A:N.285, A:D.343, A:D.343, A:G.347 Water bridges: D:T.372, A:R.275, A:R.275, A:N.348 pi-Stacking: D:Y.369 Salt bridges: A:R.275, A:R.275

4 x 4NI: 4-nitrobutanoic acid(Non-covalent)

4NI.2: 11 residues within 4Å: Chain A: R.94, S.95, S.98, V.99, L.103, F.133, T.170, L.246, Y.369, D.370 Ligands: FAD.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.103 Hydrogen bonds: A:S.98, A:D.370 4NI.4: 11 residues within 4Å: Chain B: R.94, S.95, S.98, V.99, L.103, F.133, T.170, L.246, Y.369, D.370 Ligands: FAD.3 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.103 Hydrogen bonds: B:S.98, B:D.370 4NI.6: 11 residues within 4Å: Chain C: R.94, S.95, S.98, V.99, L.103, F.133, T.170, L.246, Y.369, D.370 Ligands: FAD.5 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.103 Hydrogen bonds: C:S.98, C:D.370 4NI.8: 11 residues within 4Å: Chain D: R.94, S.95, S.98, V.99, L.103, F.133, T.170, L.246, Y.369, D.370 Ligands: FAD.7 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.103 Hydrogen bonds: D:S.98, D:D.370

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