SMTL ID : 1ivh.1

STRUCTURE OF HUMAN ISOVALERYL-COA DEHYDROGENASE AT 2.6 ANGSTROMS RESOLUTION: STRUCTURAL BASIS FOR SUBSTRATE SPECIFICITY

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: 25 residues within 4Å: Chain A: L.133, A.134, M.135, S.136, G.141, S.142, W.166, T.168, K.213, L.370, I.373, T.377, E.379, L.383 Chain B: R.280, F.283, I.287, F.290, M.293, Q.348, C.349, G.351, G.352 Chain D: Q.291 Ligands: COS.2 24 PLIP interactions: 16 interactions with chain A, 7 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: A:W.166, A:W.166, A:L.370 Hydrogen bonds: A:L.133, A:M.135, A:S.136, A:S.136, A:S.142, A:S.142, A:W.166, A:T.168, A:T.168, A:T.377, A:T.377, A:E.379, B:Q.348, B:G.352, D:Q.291 Water bridges: A:G.141, B:R.280, B:R.280, B:N.353 Salt bridges: B:R.280, B:R.280 FAD.3: 27 residues within 4Å: Chain A: R.280, F.283, I.287, F.290, L.292, M.293, Q.348, C.349, G.351, G.352 Chain B: L.133, A.134, M.135, S.136, G.141, S.142, W.166, I.167, T.168, K.213, L.370, I.373, T.377, E.379, L.383 Chain C: Q.291 Ligands: COS.4 20 PLIP interactions: 6 interactions with chain A, 13 interactions with chain B, 1 interactions with chain C Hydrogen bonds: A:Q.348, A:G.352, B:L.133, B:M.135, B:S.136, B:S.136, B:S.142, B:S.142, B:T.168, B:T.377, C:Q.291 Salt bridges: A:R.280, A:R.280 pi-Stacking: A:F.290, A:F.290 Hydrophobic interactions: B:W.166, B:W.166, B:L.370 Water bridges: B:G.141, B:G.141 FAD.5: 26 residues within 4Å: Chain B: Q.291 Chain C: L.133, A.134, M.135, S.136, G.141, S.142, W.166, I.167, T.168, K.213, L.370, I.373, T.377, E.379, L.383 Chain D: R.280, F.283, I.287, F.290, M.293, Q.348, C.349, G.351, G.352 Ligands: COS.6 22 PLIP interactions: 16 interactions with chain C, 5 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: C:W.166, C:W.166, C:K.213, C:L.370 Hydrogen bonds: C:L.133, C:M.135, C:S.136, C:S.136, C:S.142, C:S.142, C:T.168, C:T.377, D:Q.348, D:G.352, B:Q.291 Water bridges: C:L.133, C:G.141, C:G.141, C:I.373, D:N.353 Salt bridges: D:R.280, D:R.280 FAD.7: 27 residues within 4Å: Chain A: Q.291 Chain C: R.280, F.283, I.287, F.290, L.292, M.293, Q.348, C.349, G.351, G.352 Chain D: L.133, A.134, M.135, S.136, G.141, S.142, W.166, I.167, T.168, K.213, L.370, I.373, T.377, E.379, L.383 Ligands: COS.8 24 PLIP interactions: 6 interactions with chain C, 1 interactions with chain A, 17 interactions with chain D Hydrogen bonds: C:Q.348, C:G.352, A:Q.291, D:L.133, D:M.135, D:S.136, D:S.136, D:S.142, D:S.142, D:W.166, D:T.168, D:T.168, D:T.377, D:T.377, D:E.379 Water bridges: C:R.280, C:R.280, D:T.377 Salt bridges: C:R.280, C:R.280 Hydrophobic interactions: D:W.166, D:W.166, D:K.213, D:L.370

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

COS.2: 23 residues within 4Å: Chain A: M.135, S.136, G.141, S.142, V.144, V.145, S.190, R.191, V.244, Y.245, M.248, L.251, D.252, E.254, R.255, G.374, A.375, G.376, V.380, V.384, R.387 Chain B: F.283 Ligands: FAD.1 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.384, B:F.283 Hydrogen bonds: A:S.142, A:S.190, A:Y.245, A:D.252, A:R.255, A:R.387 Water bridges: A:S.136, A:G.141, A:D.252 Salt bridges: A:R.191 COS.4: 22 residues within 4Å: Chain A: F.283 Chain B: M.135, G.141, S.142, V.144, V.145, S.190, R.191, V.244, Y.245, M.248, L.251, D.252, E.254, R.255, G.374, A.375, G.376, V.380, V.384, R.387 Ligands: FAD.3 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.380, B:V.384, A:F.283 Hydrogen bonds: B:S.142, B:V.144, B:S.190, B:D.252, B:R.255, B:R.255, B:R.387 Water bridges: B:S.142 Salt bridges: B:R.191 COS.6: 21 residues within 4Å: Chain C: M.135, G.141, S.142, D.143, V.144, V.145, S.190, R.191, V.244, Y.245, M.248, L.251, E.254, R.255, G.374, A.375, G.376, V.380, R.387 Chain D: F.283 Ligands: FAD.5 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.142, C:V.144, C:S.190, C:D.252, C:R.255, C:R.387 Water bridges: C:S.136, C:A.375, C:A.375 Salt bridges: C:R.191 Hydrophobic interactions: D:F.283 COS.8: 21 residues within 4Å: Chain C: F.283 Chain D: M.135, S.136, G.141, S.142, V.144, V.145, S.190, V.244, Y.245, M.248, L.251, E.254, R.255, G.374, A.375, G.376, V.380, V.384, R.387 Ligands: FAD.7 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.384, C:F.283 Hydrogen bonds: D:S.142, D:S.190, D:S.190, D:D.252, D:R.255, D:R.387 Salt bridges: D:R.191, D:R.387

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tiffany, K.A. et al., Structure of human isovaleryl-CoA dehydrogenase at 2.6 A resolution: structural basis for substrate specificity,. Biochemistry (1997)

Release Date

1998-05-20

Peptides

ISOVALERYL-COA DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

ISOVALERYL-COA DEHYDROGENASE