SMTL ID : 4hus.1

Crystal structure of streptogramin group A antibiotic acetyltransferase VatA from Staphylococcus aureus in complex with virginiamycin M1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: E.40, R.71, F.72, W.188, L.190, M.192, I.195 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.188 Water bridges: A:Y.41, A:Y.41, A:M.192 Salt bridges: A:R.71 SO4.2: 4 residues within 4Å: Chain A: N.204 Chain C: R.89, D.113 Ligands: EDO.37 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.204 Salt bridges: C:R.89 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 Water bridges: A:K.154 Salt bridges: A:K.154 SO4.17: 4 residues within 4Å: Chain B: K.154, L.167, K.168, F.169 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.169, B:F.169 Salt bridges: B:K.154 SO4.18: 4 residues within 4Å: Chain B: K.28, G.39, E.40, R.71 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.40, B:E.40 Water bridges: B:V.38 Salt bridges: B:K.28, B:R.71 SO4.19: 2 residues within 4Å: Chain B: R.89 Chain C: N.204 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Salt bridges: B:R.89 Hydrogen bonds: C:N.204 SO4.31: 4 residues within 4Å: Chain C: K.28, G.39, E.40, R.71 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:E.40 Water bridges: C:K.28, C:E.40, C:E.40, C:R.71, C:R.71 Salt bridges: C:K.28, C:R.71 SO4.32: 4 residues within 4Å: Chain C: K.154, L.167, K.168, F.169 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:F.169 Salt bridges: C:K.154, C:K.168

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

NA.4: 5 residues within 4Å: Chain A: N.165 Chain B: N.165, P.166 Chain C: N.165, P.166 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.165, C:N.165, C:N.165

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

CL.5: 3 residues within 4Å: Chain A: G.118, D.119, K.139 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: R.101 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: R.171, K.172 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: Y.60, E.61 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain B: E.121, G.123, I.140 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain B: S.175, G.177 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain B: K.47, R.48 Ligands: EDO.11 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain C: K.47, R.48 Ligand excluded by PLIP CL.34: 1 residues within 4Å: Chain C: R.101 Ligand excluded by PLIP

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

EDO.9: 3 residues within 4Å: Chain A: G.85, N.87, H.88 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.88 EDO.10: 3 residues within 4Å: Chain A: K.47, R.48, R.130 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:K.47, A:R.48, A:R.130 Water bridges: A:D.131, C:G.78, C:T.80 EDO.11: 6 residues within 4Å: Chain A: D.54, Q.55, L.57, T.80 Chain B: R.130 Ligands: CL.22 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.54, A:Q.55, B:R.130 Water bridges: A:Q.55 EDO.12: 5 residues within 4Å: Chain A: K.139, I.140, G.141, N.155, V.156 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.139, A:V.156 EDO.23: 2 residues within 4Å: Chain B: R.214, K.215 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.214, B:R.214, B:K.215 EDO.24: 8 residues within 4Å: Chain A: M.135 Chain B: W.127, G.129, I.146, A.147, A.148 Ligands: PEG.28, PGE.30 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.127, B:A.148 EDO.25: 2 residues within 4Å: Chain B: K.154, N.155 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.155 EDO.26: 6 residues within 4Å: Chain B: E.40, R.71, W.188, L.190, D.191, M.192 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.40, B:E.40, B:L.190 Water bridges: B:M.192 EDO.27: 3 residues within 4Å: Chain B: L.57, Y.58, Y.60 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Water bridges: C:R.130, B:H.59 Hydrogen bonds: B:Y.58, B:Y.60 EDO.35: 2 residues within 4Å: Chain C: A.147, I.161 2 PLIP interactions: 2 interactions with chain C Water bridges: C:A.148, C:A.148 EDO.36: 2 residues within 4Å: Chain C: N.14, I.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.15 EDO.37: 5 residues within 4Å: Chain A: P.200 Chain C: R.89, Y.107, M.108 Ligands: SO4.2 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:P.200, C:R.89 EDO.38: 3 residues within 4Å: Chain C: N.124, Q.186, N.189 4 PLIP interactions: 4 interactions with chain C Water bridges: C:N.124, C:N.124, C:N.124, C:W.188 EDO.39: 4 residues within 4Å: Chain C: D.11, P.12, E.13, E.40 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.40 EDO.40: 3 residues within 4Å: Chain C: E.34, N.35, E.61 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.35, C:E.61

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.13: 3 residues within 4Å: Chain A: E.13, K.28, P.29 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.28 PEG.14: 6 residues within 4Å: Chain A: P.77, G.129, R.130, A.147, A.148 Chain C: Y.58 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.130, A:A.148 PEG.15: 3 residues within 4Å: Chain A: A.147, I.170 Chain C: N.87 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.87 Water bridges: C:N.87, C:K.117 PEG.28: 4 residues within 4Å: Chain B: I.145, A.147, I.170 Ligands: EDO.24 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.153, A:T.153

1 x VIR: VIRGINIAMYCIN M1(Non-covalent)

VIR.16: 16 residues within 4Å: Chain A: N.21, L.24, Y.43, D.45 Chain C: Y.58, Y.60, V.62, G.85, A.86, N.87, H.88, H.98, L.99, M.108, P.109, L.114 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:Y.60, C:Y.60, C:V.62, C:V.62, C:L.114, A:Y.43, A:D.45 Hydrogen bonds: C:N.87, A:Y.43 Salt bridges: C:H.98 Water bridges: A:D.45

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.29: 6 residues within 4Å: Chain B: G.85, H.88, L.99 Chain C: N.21, Y.43, D.45 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:G.85, C:Y.43 Water bridges: C:N.21 PGE.30: 11 residues within 4Å: Chain A: Y.58, H.88, L.99 Chain B: Y.43, D.45, G.76, W.127, I.128, G.129, R.130 Ligands: EDO.24 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.130 Water bridges: B:D.45

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

2012-11-21

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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