SMTL ID : 1w6u.1

STRUCTURE OF HUMAN DECR TERNARY COMPLEX

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 23 residues within 4Å: Chain A: G.33, T.36, G.37, L.38, S.57, R.58, K.59, C.83, D.84, V.85, R.86, N.111, A.112, A.113, I.134, I.162, T.163, K.181, P.207, G.208, P.209, I.210 Ligands: HXC.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:P.207 Hydrogen bonds: A:T.36, A:T.36, A:L.38, A:S.57, A:R.58, A:K.59, A:D.84, A:V.85, A:N.111, A:A.113, A:K.181, A:I.210 Water bridges: A:G.35, A:G.39, A:G.39, A:S.57 Salt bridges: A:R.58, A:K.59 NAP.3: 24 residues within 4Å: Chain B: G.33, T.36, G.37, L.38, S.57, R.58, K.59, C.83, D.84, V.85, R.86, N.111, A.112, A.113, I.134, I.162, T.163, T.164, K.181, P.207, G.208, P.209, I.210 Ligands: HXC.4 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:P.207 Hydrogen bonds: B:T.36, B:T.36, B:T.36, B:T.36, B:L.38, B:S.57, B:R.58, B:R.58, B:K.59, B:D.84, B:D.84, B:V.85, B:N.111, B:A.113, B:K.181, B:I.210 Water bridges: B:G.39 Salt bridges: B:R.58 NAP.5: 25 residues within 4Å: Chain C: G.33, T.36, G.37, L.38, S.57, R.58, K.59, C.83, D.84, V.85, R.86, N.111, A.112, A.113, I.134, I.162, T.163, T.164, K.181, P.207, G.208, P.209, I.210, T.212 Ligands: HXC.6 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:P.207 Hydrogen bonds: C:T.36, C:T.36, C:T.36, C:L.38, C:S.57, C:R.58, C:R.58, C:K.59, C:D.84, C:V.85, C:N.111, C:A.113, C:K.181, C:I.210, C:T.212 Water bridges: C:G.35, C:T.36, C:G.39, C:N.111, C:T.212, C:T.212 Salt bridges: C:R.58 NAP.7: 24 residues within 4Å: Chain D: G.33, T.36, G.37, L.38, S.57, R.58, K.59, C.83, D.84, V.85, N.111, A.112, A.113, I.134, I.162, T.163, T.164, K.181, P.207, G.208, P.209, I.210, T.212 Ligands: HXC.8 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:P.207 Hydrogen bonds: D:T.36, D:T.36, D:T.36, D:T.36, D:L.38, D:S.57, D:R.58, D:K.59, D:D.84, D:V.85, D:N.111, D:A.113, D:K.181, D:I.210 Water bridges: D:G.35, D:G.39, D:G.39, D:S.57 Salt bridges: D:R.58

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

HXC.2: 18 residues within 4Å: Chain A: R.58, R.86, A.113, G.114, N.115, F.116, S.124, N.126, A.127, T.130, T.164, Y.166, S.177, P.209 Chain D: E.277, F.278, E.293 Ligands: NAP.1 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:F.116, A:Y.166, A:P.209, D:F.278 Hydrogen bonds: A:N.115, A:S.124, A:N.126, A:Y.166, A:S.177, D:E.293 Water bridges: A:R.58, A:S.124, A:N.126 Salt bridges: A:R.58, A:R.86 pi-Stacking: A:F.116, A:F.116 HXC.4: 16 residues within 4Å: Chain B: R.58, R.86, A.113, G.114, N.115, F.116, I.117, L.123, S.124, N.126, A.127, T.130, I.134, Y.166 Chain C: E.293 Ligands: NAP.3 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.117, B:T.130, B:I.134 Hydrogen bonds: B:R.58, B:N.115, B:N.115, B:S.124, B:N.126, B:T.130, C:E.293 Water bridges: B:S.118, B:N.126 Salt bridges: B:R.58, B:R.86 pi-Stacking: B:F.116, B:F.116 HXC.6: 17 residues within 4Å: Chain B: E.277, F.278, E.293 Chain C: A.113, G.114, N.115, F.116, L.123, S.124, N.126, A.127, T.130, T.164, Y.166, S.177, P.209 Ligands: NAP.5 18 PLIP interactions: 16 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.116, C:Y.166, B:F.278 Hydrogen bonds: C:R.86, C:G.114, C:N.115, C:S.124, C:S.124, C:N.126, C:T.130, C:Y.166, C:S.177, B:E.293 Water bridges: C:R.58, C:S.118, C:N.126 pi-Stacking: C:F.116, C:F.116 HXC.8: 16 residues within 4Å: Chain A: F.278, E.293 Chain D: R.58, R.86, A.113, G.114, N.115, F.116, L.123, S.124, N.126, A.127, T.130, I.131, K.181 Ligands: NAP.7 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:N.115, D:F.116, A:F.278 Hydrogen bonds: D:R.58, D:R.58, D:N.115, D:S.124, D:N.126, D:K.181, A:E.293 Water bridges: D:R.58, D:N.126 Salt bridges: D:R.86 pi-Stacking: D:F.116, D:F.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alphey, M.S. et al., Structure and Reactivity of Human Mitochondrial 2,4-Dienoyl-Coa Reductase: Enzyme-Ligand Interactions in a Distinctive Short-Chain Reductase Active Site. J.Biol.Chem. (2005)

Release Date

2004-10-28

Peptides

2,4-DIENOYL-COA REDUCTASE, MITOCHONDRIAL PRECURSOR: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

2,4-DIENOYL-COA REDUCTASE, MITOCHONDRIAL PRECURSOR

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