SMTL ID : 4hur.1

Crystal structure of streptogramin group A antibiotic acetyltransferase VatA from Staphylococcus aureus in complex with acetyl coenzyme A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-trimer

Ligands

3 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.1: 24 residues within 4Å: Chain A: Y.43, S.74, I.75, G.76, W.127, I.128, G.129, R.130, I.145, A.147, A.148, G.163, G.164, I.170, R.171 Chain B: Y.58, A.86, N.87, H.88, K.117, M.135, T.153, K.154, P.166 23 PLIP interactions: 12 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:A.86, B:N.87, B:T.153, B:T.153, A:Y.43, A:R.130, A:A.148, A:A.148 Water bridges: B:N.87, B:N.87, B:T.153, B:K.154, B:K.154, A:G.164, A:G.164 Salt bridges: B:K.117, B:K.117, B:K.154, A:R.171 Hydrophobic interactions: A:Y.43, A:W.127, A:I.145, A:A.147 ACO.17: 22 residues within 4Å: Chain B: Y.43, S.74, I.75, G.76, W.127, I.128, G.129, R.130, A.147, A.148, G.163, G.164, I.170, R.171 Chain C: Y.58, A.86, N.87, H.88, K.117, M.135, T.153, P.166 21 PLIP interactions: 11 interactions with chain B, 10 interactions with chain C Hydrophobic interactions: B:Y.43, B:W.127, B:A.147, C:A.86 Hydrogen bonds: B:R.130, B:A.148, B:A.148, C:A.86, C:N.87 Water bridges: B:D.45, B:D.45, B:G.164, B:G.164, C:N.87, C:N.87, C:T.153, C:K.154 Salt bridges: B:R.171, C:K.117, C:K.117, C:K.154 ACO.26: 23 residues within 4Å: Chain A: Y.58, A.86, N.87, H.88, K.117, M.135, T.153, P.166 Chain C: Y.43, S.74, I.75, G.76, W.127, I.128, G.129, R.130, I.145, A.147, A.148, G.163, G.164, I.170, R.171 18 PLIP interactions: 9 interactions with chain C, 9 interactions with chain A Hydrophobic interactions: C:Y.43, C:W.127, C:I.145, C:A.147, A:A.86 Hydrogen bonds: C:R.130, C:A.148, A:A.86, A:N.87 Water bridges: C:G.164, C:G.164, A:N.87, A:K.117, A:K.117, A:K.117 Salt bridges: C:R.171, A:K.117, A:K.117

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: K.28, G.39, E.40, R.71 Ligands: EDO.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.40 Water bridges: A:K.28, A:K.28 Salt bridges: A:K.28, A:R.71 SO4.3: 4 residues within 4Å: Chain A: K.154, L.167, K.168, F.169 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.169 Salt bridges: A:K.154, A:K.168 SO4.4: 3 residues within 4Å: Chain A: R.89, D.113 Chain C: N.204 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:D.113, C:N.204 Salt bridges: A:R.89 SO4.27: 4 residues within 4Å: Chain C: K.28, G.39, E.40, R.71 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:E.40 Water bridges: C:K.28, C:K.28, C:K.28, C:K.28 Salt bridges: C:K.28, C:R.71

26 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 2 residues within 4Å: Chain A: Y.60, E.61 Ligand excluded by PLIP EDO.6: 2 residues within 4Å: Chain A: K.154, N.155 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: N.124, W.188, N.189 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: E.40, Y.41, R.71, W.188, L.190, M.192 Ligands: SO4.2 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: L.185, L.190, I.194, N.198, K.213, R.214, L.217 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: K.139, G.141, N.155, V.156, A.157, P.158 Ligands: EDO.12 Ligand excluded by PLIP EDO.11: 1 residues within 4Å: Chain A: R.212 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: E.121, I.122, G.123, I.140, G.141 Ligands: EDO.10 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: R.130 Chain B: D.54, Q.55 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: G.118, D.119, K.139 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain A: K.139, N.155 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain B: E.40, R.71, W.188, L.190, M.192, I.195 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain B: L.37, G.39, I.68, I.69, G.70 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain A: N.204 Chain B: R.89, D.113 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain B: G.9, P.10, D.11 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain B: K.154, K.168, F.169 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: K.139, N.155, V.156, A.157 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain C: L.167, K.168, F.169 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain C: I.31, T.32, N.33 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain C: E.121, I.122, G.123, K.139, I.140, G.141 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain C: S.110, L.111, K.112 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain C: E.34, N.35, L.37, K.66 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain C: N.124, Q.186, W.188, N.189 Ligand excluded by PLIP EDO.34: 2 residues within 4Å: Chain B: N.204 Chain C: R.89 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain C: N.87, H.88, P.96, H.98 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain B: R.130 Chain C: D.54, Q.55, L.57, T.80 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.16: 6 residues within 4Å: Chain A: N.165, P.166 Chain B: N.165, P.166 Chain C: N.165, P.166 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:N.165, C:N.165, A:N.165, B:N.165

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.24: 3 residues within 4Å: Chain B: G.118, D.119, K.139 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain B: L.57, Y.58 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stogios, P.J. et al., Potential for Reduction of Streptogramin A Resistance Revealed by Structural Analysis of Acetyltransferase VatA. Antimicrob.Agents Chemother. (2014)

Release Date

2012-11-14

Peptides

Virginiamycin A acetyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Virginiamycin A acetyltransferase

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