SMTL ID : 1sir.1

The Crystal Structure and Mechanism of Human Glutaryl-CoA Dehydrogenase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 27 residues within 4Å: Chain A: F.133, L.135, T.136, G.141, S.142, W.168, I.169, T.170, L.212, Y.369, E.370, T.372, I.375, F.390 Chain C: Q.286 Chain D: R.275, Q.277, F.278, L.282, N.285, L.287, D.343, M.344, G.346, G.347, I.350 Ligands: NBC.2 28 PLIP interactions: 19 interactions with chain A, 8 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: A:W.168, A:W.168, A:L.212, 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:E.370, A:T.372, A:T.372, A:F.390, D:D.343, D:G.347, C:Q.286 Water bridges: A:F.133, A:H.373, D:R.275, D:R.275, D:K.291, D:N.348 pi-Stacking: A:Y.369 Salt bridges: D:R.275, D:R.275 FAD.3: 27 residues within 4Å: Chain B: F.133, L.135, T.136, G.141, S.142, W.168, I.169, T.170, L.212, Y.369, E.370, T.372, I.375, F.390 Chain C: R.275, Q.277, F.278, L.282, N.285, L.287, D.343, M.344, G.346, G.347, I.350 Chain D: Q.286 Ligands: NBC.4 28 PLIP interactions: 19 interactions with chain B, 8 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: B:W.168, B:W.168, B:L.212, 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:E.370, B:T.372, B:T.372, B:F.390, C:D.343, C:G.347, D:Q.286 Water bridges: B:F.133, B:H.373, C:R.275, C:R.275, C:K.291, C:N.348 pi-Stacking: B:Y.369 Salt bridges: C:R.275, C:R.275 FAD.5: 27 residues within 4Å: Chain A: Q.286 Chain B: R.275, Q.277, F.278, L.282, N.285, L.287, 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, Y.369, E.370, T.372, I.375, F.390 Ligands: NBC.6 28 PLIP interactions: 19 interactions with chain C, 1 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: C:W.168, C:W.168, C:L.212, 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:E.370, C:T.372, C:F.390, A:Q.286, B:D.343, B:G.347 Water bridges: C:F.133, C:H.373, C:D.374, C:D.374, B:Y.271, B:R.275, B:R.275, B:K.291 pi-Stacking: C:Y.369 Salt bridges: B:R.275, B:R.275 FAD.7: 27 residues within 4Å: Chain A: R.275, Q.277, F.278, L.282, N.285, L.287, 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, Y.369, E.370, T.372, I.375, F.390 Ligands: NBC.8 28 PLIP interactions: 19 interactions with chain D, 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: D:W.168, D:W.168, D:L.212, 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:E.370, D:T.372, D:F.390, A:D.343, A:G.347, B:Q.286 Water bridges: D:F.133, D:H.373, D:D.374, D:D.374, A:Y.271, A:R.275, A:R.275, A:K.291 pi-Stacking: D:Y.369 Salt bridges: A:R.275, A:R.275

4 x NBC: S-4-NITROBUTYRYL-COA(Non-covalent)

NBC.2: 20 residues within 4Å: Chain A: R.94, S.95, S.98, V.99, L.103, G.141, S.142, P.144, T.170, F.243, G.244, L.246, N.247, R.250, P.320, Y.369, E.370, I.375, R.382 Ligands: FAD.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.103, A:F.243, A:E.370 Hydrogen bonds: A:T.170, A:N.247, A:R.250, A:E.370, A:R.382 Salt bridges: A:R.382, A:R.382 NBC.4: 20 residues within 4Å: Chain B: R.94, S.95, S.98, V.99, L.103, G.141, S.142, P.144, T.170, F.243, G.244, L.246, N.247, R.250, P.320, Y.369, E.370, I.375, R.382 Ligands: FAD.3 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.103, B:F.243, B:E.370 Hydrogen bonds: B:T.170, B:N.247, B:R.250, B:E.370, B:R.382 Salt bridges: B:R.382, B:R.382 NBC.6: 20 residues within 4Å: Chain C: R.94, S.95, S.98, V.99, L.103, G.141, S.142, P.144, T.170, F.243, G.244, L.246, N.247, R.250, P.320, Y.369, E.370, I.375, R.382 Ligands: FAD.5 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.103, C:F.243, C:E.370 Hydrogen bonds: C:T.170, C:N.247, C:R.250, C:E.370, C:R.382 Salt bridges: C:R.382, C:R.382 NBC.8: 20 residues within 4Å: Chain D: R.94, S.95, S.98, V.99, L.103, G.141, S.142, P.144, T.170, F.243, G.244, L.246, N.247, R.250, P.320, Y.369, E.370, I.375, R.382 Ligands: FAD.7 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:L.103, D:F.243, D:E.370 Hydrogen bonds: D:T.170, D:N.247, D:R.250, D:E.370, D:R.382 Salt bridges: D:R.382, D:R.382

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fu, Z. et al., Crystal Structures of Human Glutaryl-CoA Dehydrogenase with and without an Alternate Substrate: Structural Bases of Dehydrogenation and Decarboxylation Reactions. Biochemistry (2004)

Release Date

2004-09-07

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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