SMTL ID : 6u3y.1 (1 other biounit)

Structure-based discovery of a novel small-molecule inhibitor of methicillin-resistant S. aureus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

hetero-4-4-mer

Ligands

12 x PQJ: fos-choline-14(Non-covalent)

PQJ.1: 8 residues within 4Å: Chain A: N.173, W.176, Y.179, E.191, L.194, G.195, S.196, R.197 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.197 Salt bridges: A:E.191 pi-Cation interactions: A:W.176 PQJ.2: 7 residues within 4Å: Chain A: T.71, I.72, S.199, N.200, L.201, W.256, W.261 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.71, A:I.72 pi-Cation interactions: A:W.256 PQJ.3: 8 residues within 4Å: Chain A: M.172, N.174, G.175 Chain G: Q.112, V.114 Chain H: K.133, I.135, Y.137 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain H, 2 interactions with chain G Hydrogen bonds: A:G.175, G:Q.112 Water bridges: A:N.174 Hydrophobic interactions: H:I.135, G:V.114 pi-Cation interactions: H:Y.137 PQJ.21: 8 residues within 4Å: Chain C: N.173, W.176, Y.179, E.191, L.194, G.195, S.196, R.197 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.197 Salt bridges: C:E.191 pi-Cation interactions: C:W.176 PQJ.22: 7 residues within 4Å: Chain C: T.71, I.72, S.199, N.200, L.201, W.256, W.261 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.71, C:I.72 pi-Cation interactions: C:W.256 PQJ.23: 8 residues within 4Å: Chain C: M.172, N.174, G.175 Chain E: Q.112, V.114 Chain F: K.133, I.135, Y.137 6 PLIP interactions: 2 interactions with chain F, 2 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: F:I.135, E:V.114 pi-Cation interactions: F:Y.137 Hydrogen bonds: C:G.175, E:Q.112 Water bridges: C:N.174 PQJ.41: 8 residues within 4Å: Chain E: N.173, W.176, Y.179, E.191, L.194, G.195, S.196, R.197 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.197 Salt bridges: E:E.191 pi-Cation interactions: E:W.176 PQJ.42: 7 residues within 4Å: Chain E: T.71, I.72, S.199, N.200, L.201, W.256, W.261 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:T.71, E:I.72 pi-Cation interactions: E:W.256 PQJ.43: 8 residues within 4Å: Chain A: Q.112, V.114 Chain B: K.133, I.135, Y.137 Chain E: M.172, N.174, G.175 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain E, 2 interactions with chain B Hydrophobic interactions: A:V.114, B:I.135 Hydrogen bonds: A:Q.112, E:G.175 Water bridges: E:N.174 pi-Cation interactions: B:Y.137 PQJ.61: 8 residues within 4Å: Chain G: N.173, W.176, Y.179, E.191, L.194, G.195, S.196, R.197 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:R.197 Salt bridges: G:E.191 pi-Cation interactions: G:W.176 PQJ.62: 7 residues within 4Å: Chain G: T.71, I.72, S.199, N.200, L.201, W.256, W.261 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:T.71, G:I.72 pi-Cation interactions: G:W.256 PQJ.63: 8 residues within 4Å: Chain C: Q.112, V.114 Chain D: K.133, I.135, Y.137 Chain G: M.172, N.174, G.175 6 PLIP interactions: 2 interactions with chain C, 2 interactions with chain G, 2 interactions with chain D Hydrophobic interactions: C:V.114, D:I.135 Hydrogen bonds: C:Q.112, G:G.175 Water bridges: G:N.174 pi-Cation interactions: D:Y.137

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

SO4.4: 4 residues within 4Å: Chain A: D.70, T.71, I.72, S.73 Ligand excluded by PLIP SO4.5: 5 residues within 4Å: Chain A: Y.144, Q.146, K.170, P.178 Chain H: K.133 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: H.3, I.4, T.5 Chain B: K.49 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: W.176, H.185, R.197 Ligand excluded by PLIP SO4.8: 1 residues within 4Å: Chain A: Q.258 Ligand excluded by PLIP SO4.9: 2 residues within 4Å: Chain A: E.209, Y.210 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: W.25, R.232, R.263 Ligand excluded by PLIP SO4.14: 1 residues within 4Å: Chain B: K.279 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain B: S.21, S.22, D.23, K.24, H.283 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain B: K.24, W.25, R.263 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain C: D.70, T.71, I.72, S.73 Ligand excluded by PLIP SO4.25: 5 residues within 4Å: Chain C: Y.144, Q.146, K.170, P.178 Chain F: K.133 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain C: H.3, I.4, T.5 Chain D: K.49 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain C: W.176, H.185, R.197 Ligand excluded by PLIP SO4.28: 1 residues within 4Å: Chain C: Q.258 Ligand excluded by PLIP SO4.29: 2 residues within 4Å: Chain C: E.209, Y.210 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain D: W.25, R.232, R.263 Ligand excluded by PLIP SO4.34: 1 residues within 4Å: Chain D: K.279 Ligand excluded by PLIP SO4.35: 5 residues within 4Å: Chain D: S.21, S.22, D.23, K.24, H.283 Ligand excluded by PLIP SO4.36: 3 residues within 4Å: Chain D: K.24, W.25, R.263 Ligand excluded by PLIP SO4.44: 4 residues within 4Å: Chain E: D.70, T.71, I.72, S.73 Ligand excluded by PLIP SO4.45: 5 residues within 4Å: Chain B: K.133 Chain E: Y.144, Q.146, K.170, P.178 Ligand excluded by PLIP SO4.46: 4 residues within 4Å: Chain E: H.3, I.4, T.5 Chain F: K.49 Ligand excluded by PLIP SO4.47: 3 residues within 4Å: Chain E: W.176, H.185, R.197 Ligand excluded by PLIP SO4.48: 1 residues within 4Å: Chain E: Q.258 Ligand excluded by PLIP SO4.49: 2 residues within 4Å: Chain E: E.209, Y.210 Ligand excluded by PLIP SO4.53: 3 residues within 4Å: Chain F: W.25, R.232, R.263 Ligand excluded by PLIP SO4.54: 1 residues within 4Å: Chain F: K.279 Ligand excluded by PLIP SO4.55: 5 residues within 4Å: Chain F: S.21, S.22, D.23, K.24, H.283 Ligand excluded by PLIP SO4.56: 3 residues within 4Å: Chain F: K.24, W.25, R.263 Ligand excluded by PLIP SO4.64: 4 residues within 4Å: Chain G: D.70, T.71, I.72, S.73 Ligand excluded by PLIP SO4.65: 5 residues within 4Å: Chain D: K.133 Chain G: Y.144, Q.146, K.170, P.178 Ligand excluded by PLIP SO4.66: 4 residues within 4Å: Chain G: H.3, I.4, T.5 Chain H: K.49 Ligand excluded by PLIP SO4.67: 3 residues within 4Å: Chain G: W.176, H.185, R.197 Ligand excluded by PLIP SO4.68: 1 residues within 4Å: Chain G: Q.258 Ligand excluded by PLIP SO4.69: 2 residues within 4Å: Chain G: E.209, Y.210 Ligand excluded by PLIP SO4.73: 3 residues within 4Å: Chain H: W.25, R.232, R.263 Ligand excluded by PLIP SO4.74: 1 residues within 4Å: Chain H: K.279 Ligand excluded by PLIP SO4.75: 5 residues within 4Å: Chain H: S.21, S.22, D.23, K.24, H.283 Ligand excluded by PLIP SO4.76: 3 residues within 4Å: Chain H: K.24, W.25, R.263 Ligand excluded by PLIP

28 x ACT: ACETATE ION(Non-functional Binders)

ACT.10: 3 residues within 4Å: Chain A: N.265, Y.266, K.267 Ligand excluded by PLIP ACT.11: 5 residues within 4Å: Chain A: K.81, R.181, E.248, K.267, D.268 Ligand excluded by PLIP ACT.12: 2 residues within 4Å: Chain A: A.1 Chain B: Q.140 Ligand excluded by PLIP ACT.17: 3 residues within 4Å: Chain B: T.66, D.67, H.68 Ligand excluded by PLIP ACT.18: 2 residues within 4Å: Chain B: K.279, K.281 Ligand excluded by PLIP ACT.19: 4 residues within 4Å: Chain B: F.76, H.173, H.257 Chain E: Y.210 Ligand excluded by PLIP ACT.20: 1 residues within 4Å: Chain B: R.148 Ligand excluded by PLIP ACT.30: 3 residues within 4Å: Chain C: N.265, Y.266, K.267 Ligand excluded by PLIP ACT.31: 5 residues within 4Å: Chain C: K.81, R.181, E.248, K.267, D.268 Ligand excluded by PLIP ACT.32: 2 residues within 4Å: Chain C: A.1 Chain D: Q.140 Ligand excluded by PLIP ACT.37: 3 residues within 4Å: Chain D: T.66, D.67, H.68 Ligand excluded by PLIP ACT.38: 2 residues within 4Å: Chain D: K.279, K.281 Ligand excluded by PLIP ACT.39: 4 residues within 4Å: Chain D: F.76, H.173, H.257 Chain G: Y.210 Ligand excluded by PLIP ACT.40: 1 residues within 4Å: Chain D: R.148 Ligand excluded by PLIP ACT.50: 3 residues within 4Å: Chain E: N.265, Y.266, K.267 Ligand excluded by PLIP ACT.51: 5 residues within 4Å: Chain E: K.81, R.181, E.248, K.267, D.268 Ligand excluded by PLIP ACT.52: 2 residues within 4Å: Chain E: A.1 Chain F: Q.140 Ligand excluded by PLIP ACT.57: 3 residues within 4Å: Chain F: T.66, D.67, H.68 Ligand excluded by PLIP ACT.58: 2 residues within 4Å: Chain F: K.279, K.281 Ligand excluded by PLIP ACT.59: 4 residues within 4Å: Chain C: Y.210 Chain F: F.76, H.173, H.257 Ligand excluded by PLIP ACT.60: 1 residues within 4Å: Chain F: R.148 Ligand excluded by PLIP ACT.70: 3 residues within 4Å: Chain G: N.265, Y.266, K.267 Ligand excluded by PLIP ACT.71: 5 residues within 4Å: Chain G: K.81, R.181, E.248, K.267, D.268 Ligand excluded by PLIP ACT.72: 2 residues within 4Å: Chain G: A.1 Chain H: Q.140 Ligand excluded by PLIP ACT.77: 3 residues within 4Å: Chain H: T.66, D.67, H.68 Ligand excluded by PLIP ACT.78: 2 residues within 4Å: Chain H: K.279, K.281 Ligand excluded by PLIP ACT.79: 4 residues within 4Å: Chain A: Y.210 Chain H: F.76, H.173, H.257 Ligand excluded by PLIP ACT.80: 1 residues within 4Å: Chain H: R.148 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, J. et al., Structure-based discovery of a small-molecule inhibitor of methicillin-resistantStaphylococcus aureusvirulence. J.Biol.Chem. (2020)

Release Date

2020-03-25

Peptides

Panton-Valentine Leucocidin F: ACEG
Gamma-hemolysin subunit A: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

B
B

D
B

F
B

H
B

Panton-Valentine Leucocidin F

Gamma-hemolysin subunit A

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