SMTL ID : 3mpj.1 (1 other biounit)

Structure of the glutaryl-coenzyme A dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

2 x LYS- GLY- HIS- HIS- HIS- HIS- HIS- HIS: Octapeptide(Non-covalent)

LYS-GLY-HIS-HIS-HIS-HIS-HIS-HIS.1: 12 residues within 4Å: Chain B: E.34, N.35, H.36, F.37, Y.39, E.121, L.123, A.164, Q.165, D.167, R.192, N.193 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.39 Hydrogen bonds: B:F.37, B:N.193, B:N.193, B:N.193 Water bridges: B:N.201 pi-Stacking: B:H.36 LYS-GLY-HIS-HIS-HIS-HIS-HIS-HIS.6: 12 residues within 4Å: Chain D: E.34, N.35, H.36, F.37, Y.39, E.121, L.123, A.164, Q.165, D.167, R.192, N.193 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Y.39 Hydrogen bonds: D:F.37, D:N.193, D:N.193, D:N.193 Water bridges: D:N.201 pi-Stacking: D:H.36

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

FAD.2: 29 residues within 4Å: Chain A: M.92, F.126, I.128, T.129, G.134, S.135, W.159, I.160, S.161, K.204, M.365, V.366, E.367, S.369, N.371, I.372, M.375 Chain B: Q.282 Chain D: R.271, Q.273, F.274, I.278, F.281, N.284, R.340, I.341, G.343, A.344, Y.345 29 PLIP interactions: 2 interactions with chain B, 18 interactions with chain A, 9 interactions with chain D Hydrogen bonds: B:Q.282, A:F.126, A:I.128, A:T.129, A:T.129, A:T.129, A:S.135, A:S.161, A:E.367, A:S.369, A:S.369, A:N.371, D:Q.273, D:N.284, D:R.340, D:A.344 Water bridges: B:Q.282, A:F.126, A:G.368, A:N.371, D:R.271, D:R.271 Hydrophobic interactions: A:W.159, A:W.159, A:K.204, A:V.366, D:A.344 Salt bridges: D:R.271, D:R.271 FAD.4: 29 residues within 4Å: Chain A: Q.282 Chain B: M.92, F.126, I.128, T.129, G.134, S.135, W.159, I.160, S.161, K.204, M.365, V.366, E.367, S.369, N.371, I.372, M.375 Chain C: R.271, Q.273, F.274, I.278, F.281, N.284, R.340, I.341, G.343, A.344, Y.345 27 PLIP interactions: 17 interactions with chain B, 1 interactions with chain A, 9 interactions with chain C Hydrophobic interactions: B:W.159, B:K.204, B:V.366, C:A.344 Hydrogen bonds: B:F.126, B:I.128, B:T.129, B:T.129, B:T.129, B:S.135, B:S.161, B:E.367, B:S.369, B:S.369, B:N.371, A:Q.282, C:Q.273, C:N.284, C:R.340, C:A.344 Water bridges: B:F.126, B:G.368, B:N.371, C:R.271, C:R.271 Salt bridges: C:R.271, C:R.271 FAD.7: 29 residues within 4Å: Chain B: R.271, Q.273, F.274, I.278, F.281, N.284, R.340, I.341, G.343, A.344, Y.345 Chain C: M.92, F.126, I.128, T.129, G.134, S.135, W.159, I.160, S.161, K.204, M.365, V.366, E.367, S.369, N.371, I.372, M.375 Chain D: Q.282 29 PLIP interactions: 9 interactions with chain B, 18 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: B:A.344, C:W.159, C:W.159, C:K.204, C:V.366 Hydrogen bonds: B:Q.273, B:N.284, B:R.340, B:A.344, C:F.126, C:I.128, C:T.129, C:T.129, C:T.129, C:S.135, C:S.161, C:E.367, C:S.369, C:S.369, C:N.371, D:Q.282 Water bridges: B:R.271, B:R.271, C:F.126, C:G.368, C:N.371, D:Q.282 Salt bridges: B:R.271, B:R.271 FAD.9: 29 residues within 4Å: Chain A: R.271, Q.273, F.274, I.278, F.281, N.284, R.340, I.341, G.343, A.344, Y.345 Chain C: Q.282 Chain D: M.92, F.126, I.128, T.129, G.134, S.135, W.159, I.160, S.161, K.204, M.365, V.366, E.367, S.369, N.371, I.372, M.375 27 PLIP interactions: 17 interactions with chain D, 9 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: D:W.159, D:K.204, D:V.366, A:A.344 Hydrogen bonds: D:F.126, D:I.128, D:T.129, D:T.129, D:T.129, D:S.135, D:S.161, D:E.367, D:S.369, D:S.369, D:N.371, A:Q.273, A:N.284, A:R.340, A:A.344, C:Q.282 Water bridges: D:F.126, D:G.368, D:N.371, A:R.271, A:R.271 Salt bridges: A:R.271, A:R.271

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

CL.3: 3 residues within 4Å: Chain A: N.35, K.204, H.208 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain B: N.35, K.204, H.208 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain C: N.35, K.204, H.208 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain D: N.35, K.204, H.208 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wischgoll, S. et al., Structural basis for promoting and preventing decarboxylation in glutaryl-coenzyme a dehydrogenases. Biochemistry (2010)

Release Date

2010-08-18

Peptides

Glutaryl-CoA dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Glutaryl-CoA dehydrogenase

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