SMTL ID : 5egl.1

The structural and biochemical characterization of acyl-coa hydrolase from Staphylococcus aureus in complex with Butyryl Coenzyme A, Coenzyme A, and Coenzyme A disulfide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

2 x BCO: Butyryl Coenzyme A(Non-covalent)

BCO.1: 32 residues within 4Å: Chain A: A.47, V.58, V.59, T.60, A.61, S.62, D.64, G.88, T.89, S.90, S.91, T.117, V.119, L.121, P.127, R.154, K.155, R.157, R.158 Chain B: N.28, T.32, M.33, F.34, G.35, L.38, D.67, F.68, L.69, K.70, P.71, I.72 Chain D: Q.21 23 PLIP interactions: 15 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:V.59, A:A.61, A:V.119, B:F.68 Hydrogen bonds: A:A.61, A:T.89, A:S.90, A:S.91, A:S.91, A:R.154, A:R.157, A:R.158, A:R.158, B:M.33, B:D.67, B:F.68, B:L.69, B:I.72 Water bridges: A:K.155, B:N.28, B:N.28 Salt bridges: A:R.158 pi-Cation interactions: A:R.158 BCO.4: 32 residues within 4Å: Chain A: Q.21 Chain D: A.47, V.58, V.59, T.60, A.61, S.62, D.64, G.88, T.89, S.90, S.91, T.117, V.119, L.121, P.127, R.154, K.155, R.157, R.158 Chain E: N.28, T.32, M.33, F.34, G.35, L.38, D.67, F.68, L.69, K.70, P.71, I.72 22 PLIP interactions: 15 interactions with chain D, 7 interactions with chain E Hydrophobic interactions: D:V.59, D:A.61, D:V.119, E:F.68 Hydrogen bonds: D:A.61, D:T.89, D:S.90, D:S.91, D:S.91, D:R.154, D:R.157, D:R.158, D:R.158, E:M.33, E:F.68, E:L.69, E:I.72 Water bridges: D:K.155, E:N.28, E:N.28 Salt bridges: D:R.158 pi-Cation interactions: D:R.158

2 x COA: COENZYME A(Non-covalent)

COA.2: 25 residues within 4Å: Chain A: N.28, T.32, M.33, F.34, G.35, D.67, F.68, L.69, K.70, P.71, I.72 Chain B: V.59, T.60, A.61, S.62, G.88, T.89, S.90, S.91, T.117, V.119, L.121, P.127, R.154, R.158 18 PLIP interactions: 14 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:V.59 Hydrogen bonds: B:T.60, B:A.61, B:T.89, B:S.90, B:S.91, B:S.91, B:S.91, B:R.154, B:R.154, B:R.158, B:R.158, A:M.33, A:L.69, A:L.69 Water bridges: B:K.155, B:K.155, A:F.68 COA.5: 25 residues within 4Å: Chain D: N.28, T.32, M.33, F.34, G.35, D.67, F.68, L.69, K.70, P.71, I.72 Chain E: V.59, T.60, A.61, S.62, G.88, T.89, S.90, S.91, T.117, V.119, L.121, P.127, R.154, R.158 18 PLIP interactions: 14 interactions with chain E, 4 interactions with chain D Hydrophobic interactions: E:V.59 Hydrogen bonds: E:T.60, E:A.61, E:T.89, E:S.90, E:S.91, E:S.91, E:S.91, E:R.154, E:R.154, E:R.158, E:R.158, D:M.33, D:L.69, D:L.69 Water bridges: E:K.155, E:K.155, D:F.68

2 x 5NG: [[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{R})-4-[[3-[2-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyldisulfanyl]ethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate(Non-covalent)

5NG.3: 49 residues within 4Å: Chain A: Q.25, F.34, G.35, G.36, T.37 Chain B: K.18, R.20, Q.21, F.23, Q.25, T.37, A.40, N.41, D.43, E.44 Chain C: K.18, R.20, F.23, D.43, E.44, A.47, V.59, T.60, A.61, S.62, G.88, T.89, S.90, S.91, T.117, F.118, V.119, L.121, P.127, R.154, K.155, R.157, R.158 Chain F: N.28, T.32, M.33, F.34, G.35, D.67, F.68, L.69, K.70, P.71, I.72 41 PLIP interactions: 23 interactions with chain C, 4 interactions with chain F, 9 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: C:A.47, C:V.59, C:A.61, F:F.34, F:F.68, B:F.23 Hydrogen bonds: C:T.60, C:T.60, C:S.62, C:T.89, C:S.90, C:S.90, C:S.90, C:S.91, C:S.91, C:R.158, F:D.67, B:Q.21, B:N.41, B:D.43, B:D.43, A:G.36, A:T.37 Water bridges: C:D.43, C:D.43, C:E.44, C:V.58, F:I.72, B:K.18, B:R.20, B:R.20, A:G.35 Salt bridges: C:K.18, C:R.20, C:R.20, C:K.155, C:R.158, C:R.158, B:R.20 pi-Stacking: A:F.34, A:F.34 5NG.6: 49 residues within 4Å: Chain C: N.28, T.32, M.33, F.34, G.35, D.67, F.68, L.69, K.70, P.71, I.72 Chain D: Q.25, F.34, G.35, G.36, T.37 Chain E: K.18, R.20, Q.21, F.23, Q.25, T.37, A.40, N.41, D.43, E.44 Chain F: K.18, R.20, F.23, D.43, E.44, A.47, V.59, T.60, A.61, S.62, G.88, T.89, S.90, S.91, T.117, F.118, V.119, L.121, P.127, R.154, K.155, R.157, R.158 42 PLIP interactions: 24 interactions with chain F, 5 interactions with chain D, 4 interactions with chain C, 9 interactions with chain E Hydrophobic interactions: F:A.47, F:V.59, F:A.61, C:F.34, C:F.68, E:F.23 Hydrogen bonds: F:T.60, F:T.60, F:S.62, F:S.62, F:T.89, F:S.90, F:S.90, F:S.90, F:S.91, F:S.91, F:R.158, D:G.36, D:T.37, C:D.67, E:Q.21, E:N.41, E:D.43, E:E.44 Water bridges: F:K.18, F:D.43, F:E.44, F:V.58, D:G.35, C:I.72, E:K.18, E:R.20, E:R.20 Salt bridges: F:K.18, F:R.20, F:R.20, F:K.155, F:R.158, F:R.158, E:R.20 pi-Stacking: D:F.34, D:F.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Khandokar, Y.B. et al., The structural and biochemical characterization of acyl-coa hydrolase from Staphylococcus aureus. To Be Published

Release Date

2016-11-09

Peptides

Acyl CoA Hydrolase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Acyl CoA Hydrolase