SMTL ID : 4fc6.1

Studies on DCR shed new light on peroxisomal beta-oxidation: Crystal structure of the ternary complex of pDCR

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 28 residues within 4Å: Chain A: G.34, S.37, G.38, I.39, S.58, R.59, S.60, R.63, M.84, D.85, V.86, R.87, C.112, A.113, A.114, I.135, I.162, T.163, K.181, P.207, G.208, P.209, I.210, T.213, E.214, G.215, L.216 Ligands: HXC.2 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:P.207 Hydrogen bonds: A:S.37, A:S.37, A:S.37, A:I.39, A:S.58, A:R.59, A:S.60, A:D.85, A:V.86, A:R.87, A:C.112, A:A.114, A:K.181, A:I.210, A:T.213, A:T.213, A:G.215, A:L.216 Water bridges: A:S.37, A:G.40, A:R.59, A:R.59, A:E.214, A:E.214 Salt bridges: A:R.59, A:R.63 NAP.3: 28 residues within 4Å: Chain B: G.34, S.37, G.38, I.39, S.58, R.59, S.60, R.63, M.84, D.85, V.86, R.87, C.112, A.113, A.114, I.135, I.162, T.163, K.181, P.207, G.208, P.209, I.210, T.213, E.214, G.215, L.216 Ligands: HXC.4 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:P.207 Hydrogen bonds: B:S.37, B:S.37, B:S.37, B:I.39, B:S.58, B:R.59, B:S.60, B:D.85, B:V.86, B:R.87, B:C.112, B:A.114, B:K.181, B:I.210, B:T.213, B:G.215, B:L.216 Water bridges: B:D.10, B:G.36, B:S.37, B:S.37, B:G.40, B:G.40, B:R.63, B:R.63, B:E.214 Salt bridges: B:R.59, B:R.63 pi-Cation interactions: B:R.59 NAP.6: 28 residues within 4Å: Chain C: G.34, S.37, G.38, I.39, S.58, R.59, S.60, R.63, M.84, D.85, V.86, R.87, C.112, A.113, A.114, I.135, I.162, T.163, K.181, P.207, G.208, P.209, I.210, T.213, E.214, G.215, L.216 Ligands: HXC.5 27 PLIP interactions: 27 interactions with chain C Hydrophobic interactions: C:P.207 Hydrogen bonds: C:S.37, C:S.37, C:S.37, C:I.39, C:S.58, C:R.59, C:S.60, C:D.85, C:V.86, C:R.87, C:C.112, C:A.114, C:K.181, C:I.210, C:T.213, C:G.215, C:L.216 Water bridges: C:S.37, C:G.40, C:R.59, C:R.59, C:R.63, C:R.63, C:R.63 Salt bridges: C:R.59, C:R.63 NAP.7: 28 residues within 4Å: Chain D: G.34, S.37, G.38, I.39, S.58, R.59, S.60, R.63, M.84, D.85, V.86, R.87, C.112, A.113, A.114, I.135, I.162, T.163, K.181, P.207, G.208, P.209, I.210, T.213, E.214, G.215, L.216 Ligands: HXC.8 30 PLIP interactions: 30 interactions with chain D Hydrophobic interactions: D:P.207 Hydrogen bonds: D:S.37, D:S.37, D:S.37, D:I.39, D:S.58, D:R.59, D:S.60, D:D.85, D:V.86, D:R.87, D:C.112, D:A.114, D:K.181, D:I.210, D:T.213, D:T.213, D:G.215, D:L.216 Water bridges: D:G.36, D:S.37, D:G.40, D:G.40, D:R.59, D:R.59, D:R.59, D:R.63, D:E.214 Salt bridges: D:R.59, D:R.63

4 x HXC: HEXANOYL-COENZYME A(Non-covalent)

HXC.2: 18 residues within 4Å: Chain A: R.59, R.87, A.114, G.115, N.116, F.117, L.118, C.119, S.125, N.127, A.128, T.131, L.166, E.214, G.215, R.218, L.219 Ligands: NAP.1 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:N.116, A:F.117, A:L.166, A:L.166, A:L.219 Hydrogen bonds: A:R.59, A:R.59, A:N.116, A:N.116, A:S.125, A:N.127, A:R.218, A:R.218 Water bridges: A:R.87, A:R.87, A:R.87, A:R.87, A:L.118, A:F.126 Salt bridges: A:R.59, A:R.87 pi-Stacking: A:F.117, A:F.117 HXC.4: 19 residues within 4Å: Chain B: R.59, R.87, G.115, N.116, F.117, C.119, S.125, N.127, A.128, T.131, I.135, A.164, L.166, K.181, E.214, G.215, R.218, L.219 Ligands: NAP.3 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:F.117, B:I.135, B:A.164, B:L.166, B:L.166 Hydrogen bonds: B:R.59, B:R.59, B:N.116, B:N.116, B:S.125, B:S.125, B:N.127, B:R.218 Water bridges: B:R.87, B:L.118, B:R.218 Salt bridges: B:R.87 pi-Stacking: B:F.117, B:F.117 HXC.5: 19 residues within 4Å: Chain C: R.59, R.87, A.114, G.115, N.116, F.117, L.118, C.119, S.125, N.127, A.128, T.131, I.135, L.166, E.214, G.215, R.218, L.219 Ligands: NAP.6 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:L.166, C:L.166, C:L.219 Hydrogen bonds: C:R.59, C:R.59, C:N.116, C:S.125, C:N.127, C:R.218, C:R.218 Water bridges: C:R.87, C:R.87, C:G.115, C:L.118, C:L.118, C:L.118, C:S.125, C:F.126 Salt bridges: C:R.59, C:R.87 pi-Stacking: C:F.117, C:F.117 HXC.8: 19 residues within 4Å: Chain D: R.59, R.87, A.114, G.115, N.116, F.117, L.118, C.119, S.125, N.127, A.128, T.131, I.135, L.166, E.214, G.215, R.218, L.219 Ligands: NAP.7 24 PLIP interactions: 24 interactions with chain D Hydrophobic interactions: D:N.116, D:F.117, D:I.135, D:L.166, D:L.219 Hydrogen bonds: D:R.59, D:R.59, D:N.116, D:N.116, D:S.125, D:N.127, D:R.218, D:R.218 Water bridges: D:R.87, D:R.87, D:R.87, D:L.118, D:L.118, D:S.125, D:N.127 Salt bridges: D:R.59, D:R.87 pi-Stacking: D:F.117, D:F.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hua, T. et al., Studies of human 2,4-dienoyl CoA reductase shed new light on peroxisomal beta-oxidation of unsaturated fatty acids. J.Biol.Chem. (2012)

Release Date

2012-07-04

Peptides

Peroxisomal 2,4-dienoyl-CoA reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Peroxisomal 2,4-dienoyl-CoA reductase

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