SMTL ID : 4n5m.1

Crystal structure of (R)-3-hydroxybutyryl-CoA dehydrogenase from Ralstonia eutropha in complexed with acetoacetyl-CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.34 Å

Oligo State

homo-tetramer

Ligands

4 x CAA: ACETOACETYL-COENZYME A(Non-covalent)

CAA.1: 16 residues within 4Å: Chain A: T.116, D.118, Q.171, F.172, G.173, Q.174, Y.177, G.208, Y.209, I.210, M.214, V.215, I.218, R.219, V.222, I.226 14 PLIP interactions: 1 interactions with chain B, 13 interactions with chain A Water bridges: B:Q.193, A:D.118, A:Q.171, A:F.172 Hydrophobic interactions: A:Y.209 Hydrogen bonds: A:D.118, A:Q.171, A:Q.174, A:Y.209, A:I.210 Salt bridges: A:R.219, A:R.219 pi-Stacking: A:F.172, A:F.172 CAA.5: 17 residues within 4Å: Chain B: T.116, D.118, S.164, N.166, Q.171, F.172, G.173, Q.174, Y.177, G.208, Y.209, M.214, V.215, I.218, R.219, V.222, I.226 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.209 Hydrogen bonds: B:D.118, B:Q.171, B:Q.171, B:Q.174, B:Y.209, B:I.210 Water bridges: B:D.118, B:F.172 Salt bridges: B:R.219, B:R.219 pi-Stacking: B:F.172, B:F.172 CAA.9: 16 residues within 4Å: Chain C: T.116, D.118, Q.171, F.172, G.173, Q.174, Y.177, G.208, Y.209, I.210, M.214, V.215, I.218, R.219, V.222, I.226 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Y.209 Hydrogen bonds: C:D.118, C:Q.171, C:Q.174, C:I.210 Water bridges: C:Q.171, C:F.172, D:Q.193 Salt bridges: C:R.219, C:R.219 pi-Stacking: C:F.172, C:F.172 CAA.13: 17 residues within 4Å: Chain D: T.116, D.118, S.164, N.166, Q.171, F.172, G.173, Q.174, Y.177, G.208, Y.209, M.214, V.215, I.218, R.219, V.222, I.226 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:Y.209 Hydrogen bonds: D:D.118, D:Q.171, D:Q.171, D:Q.174, D:I.210 Water bridges: D:F.172 Salt bridges: D:R.219, D:R.219 pi-Stacking: D:F.172, D:F.172

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: T.125, R.126 Chain B: W.89 Ligands: GOL.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.126 Water bridges: A:A.127 GOL.3: 7 residues within 4Å: Chain A: R.122, K.123, M.124, T.125 Chain B: W.89, K.145 Ligands: GOL.2 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.123, B:K.145 Water bridges: B:K.145 GOL.4: 5 residues within 4Å: Chain A: G.84, N.85, V.86, A.113, T.135 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.34, A:V.86 Water bridges: A:G.59, A:N.85 GOL.6: 5 residues within 4Å: Chain B: Q.27, R.28, D.50, G.51, F.52 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.28, B:G.51 Water bridges: B:D.50, B:E.251, B:E.251 GOL.7: 10 residues within 4Å: Chain B: Y.31, T.33, G.34, G.57, C.58, G.59, S.82, G.84, V.86, A.113 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.34, B:C.58 Water bridges: B:G.59, B:G.84 GOL.8: 3 residues within 4Å: Chain B: G.59, P.60, N.85 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.59 GOL.10: 4 residues within 4Å: Chain C: T.125, R.126 Chain D: W.89 Ligands: GOL.11 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.126 Water bridges: C:A.127 GOL.11: 7 residues within 4Å: Chain C: R.122, K.123, M.124, T.125 Chain D: W.89, K.145 Ligands: GOL.10 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:K.145, C:K.123 Water bridges: D:K.145 GOL.12: 5 residues within 4Å: Chain C: G.84, N.85, V.86, A.113, T.135 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.34, C:V.86 Water bridges: C:G.59, C:N.85 GOL.14: 5 residues within 4Å: Chain D: Q.27, R.28, D.50, G.51, F.52 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.28, D:G.51 Water bridges: D:D.50, D:E.251, D:E.251 GOL.15: 10 residues within 4Å: Chain D: Y.31, T.33, G.34, G.57, C.58, G.59, S.82, G.84, V.86, A.113 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Y.31, D:G.34, D:C.58 Water bridges: D:G.59, D:G.84 GOL.16: 3 residues within 4Å: Chain D: G.59, P.60, N.85 1 PLIP interactions: 1 interactions with chain D Water bridges: D:G.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, J.-E. et al., Crystal structure of (R)-3-hydroxybutyryl-CoA dehydrogenase PhaB from Ralstonia eutropha. Biochem.Biophys.Res.Commun. (2014)

Release Date

2013-12-11

Peptides

Acetoacetyl-CoA reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Acetoacetyl-CoA reductase

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