SMTL ID : 6x3j.1 (1 other biounit)

Crystal structure of streptogramin A acetyltransferase VatA from Staphylococcus aureus in complex with streptogramin analog F0224 (46)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-trimer

Ligands

3 x O7V: (2R)-2-[(3S,4R,5E,10E,12E,14S,16R,26aR)-16-fluoro-14-hydroxy-4,12-dimethyl-1,7,22-trioxo-4,7,8,9,14,15,16,17,24,25,26,26a-dodecahydro-1H,3H,22H-21,18-(azeno)pyrrolo[2,1-c][1,8,4,19]dioxadiazacyclotetracosin-3-yl]propyl isoquinolin-3-ylcarbamate(Non-covalent)

O7V.1: 23 residues within 4Å: Chain A: Y.51, Y.53, E.54, V.55, I.56, G.78, A.79, N.80, H.81, R.82, P.89, H.91, L.92, M.101, P.102, L.104, L.107 Chain C: I.11, N.14, L.17, Y.36, D.38 Ligands: SXA.10 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.51, A:Y.53, A:V.55, A:V.55, A:I.56, A:P.102, A:L.104 Hydrogen bonds: A:H.81, A:H.91 Salt bridges: A:H.91 O7V.4: 24 residues within 4Å: Chain B: I.11, N.14, L.17, Y.36, D.38, S.67 Chain C: Y.51, Y.53, V.55, I.56, G.78, A.79, N.80, H.81, R.82, P.89, H.91, L.92, R.94, M.101, P.102, L.104, L.107 Ligands: SXA.8 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:Y.51, C:Y.53, C:Y.53, C:L.92, C:P.102, B:L.17 Hydrogen bonds: C:H.91, B:Y.36 Salt bridges: C:H.91 pi-Cation interactions: C:R.94 Water bridges: B:N.14 O7V.5: 24 residues within 4Å: Chain A: I.11, N.14, L.17, Y.36, D.38, S.67 Chain B: Y.51, Y.53, E.54, V.55, I.56, G.78, A.79, N.80, H.81, R.82, P.89, H.91, L.92, M.101, P.102, L.104, L.107 Ligands: SXA.3 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.51, B:Y.53, B:Y.53, B:V.55, B:P.102, B:L.107 Hydrogen bonds: B:H.81, B:H.91, A:Y.36 Salt bridges: B:H.91 Water bridges: A:N.14

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 4 residues within 4Å: Chain A: G.198, D.199, I.200, E.201 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.199, A:D.199, A:I.200

3 x SXA: THIOACETIC ACID S-{2-[3-(2-HYDROXY-3,3-DIMETHYL-4-PHOSPHONOOXY-BUTYRYLAMINO)-PROPIONYLAMINO]-ETHYL} ESTER(Non-covalent)

SXA.3: 26 residues within 4Å: Chain A: Y.36, D.38, S.67, I.68, G.69, P.70, W.120, I.121, G.122, R.123, I.138, A.140, A.141, I.154, I.163, R.164 Chain B: Y.51, I.75, A.79, N.80, H.81, M.83, P.108, K.110, M.128 Ligands: O7V.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.141 SXA.8: 23 residues within 4Å: Chain B: S.67, G.69, P.70, W.120, I.121, G.122, R.123, I.138, A.140, A.141, I.154, R.164 Chain C: Y.51, I.75, A.79, N.80, H.81, M.83, P.108, K.110, M.128, P.129 Ligands: O7V.4 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.154 Hydrogen bonds: B:W.120, B:A.141 SXA.10: 26 residues within 4Å: Chain A: Y.51, I.75, A.79, N.80, H.81, M.83, P.108, K.110, P.129 Chain C: Y.36, S.67, I.68, G.69, P.70, W.120, I.121, G.122, R.123, I.138, I.139, A.140, A.141, I.154, I.163, R.164 Ligands: O7V.1 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:Y.36, C:W.120, C:A.141, A:N.80, A:H.81

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

CL.6: 2 residues within 4Å: Chain B: L.50, Y.51 Ligand excluded by PLIP CL.7: 6 residues within 4Å: Chain B: I.56, D.58, N.77, L.109, K.110, G.111 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 8 residues within 4Å: Chain A: N.158, P.159, K.161 Chain B: N.158, P.159, K.161 Chain C: N.158, P.159 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:N.158, B:N.158, H2O.1, H2O.2, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Q. et al., Synthetic group A streptogramin antibiotics that overcome Vat resistance. Nature (2020)

Release Date

2020-11-18

Peptides

Virginiamycin A acetyltransferase,VatA: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

Virginiamycin A acetyltransferase,VatA

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