SMTL ID : 6u4p.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

homo-heptamer

Ligands

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

PQJ.1: 9 residues within 4Å: Chain A: N.176, Q.177, W.179, Y.182, Q.194, M.197, K.198, T.199, R.200 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.200 Salt bridges: A:R.200 pi-Cation interactions: A:W.179 PQJ.2: 8 residues within 4Å: Chain A: W.179, G.180, P.181, Y.182, N.188, Q.194 Chain G: H.144 Ligands: SO4.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.182, A:Y.182, A:N.188, A:Q.194 PQJ.10: 9 residues within 4Å: Chain B: N.176, Q.177, W.179, Y.182, Q.194, M.197, K.198, T.199, R.200 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.198, B:R.200 pi-Cation interactions: B:W.179 PQJ.11: 9 residues within 4Å: Chain A: H.144 Chain B: W.179, G.180, P.181, Y.182, N.188, Q.194, R.200 Ligands: SO4.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.182, B:N.188, B:Q.194, B:R.200 PQJ.15: 9 residues within 4Å: Chain C: N.176, Q.177, W.179, Y.182, Q.194, M.197, K.198, T.199, R.200 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.200 pi-Cation interactions: C:W.179 PQJ.16: 8 residues within 4Å: Chain C: W.179, G.180, P.181, Y.182, N.188, Q.194, R.200 Ligands: SO4.17 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.188, C:Q.194 Salt bridges: C:R.200 PQJ.22: 9 residues within 4Å: Chain D: N.176, Q.177, W.179, Y.182, Q.194, M.197, K.198, T.199, R.200 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.200 pi-Cation interactions: D:W.179 PQJ.23: 6 residues within 4Å: Chain C: H.144 Chain D: Y.182, N.188, Q.194, R.200 Ligands: SO4.24 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.188, D:Q.194, D:R.200 PQJ.27: 9 residues within 4Å: Chain E: N.176, Q.177, W.179, Y.182, Q.194, M.197, K.198, T.199, R.200 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.200 pi-Cation interactions: E:W.179 PQJ.28: 7 residues within 4Å: Chain E: G.180, P.181, Y.182, N.188, Q.194, R.200 Ligands: SO4.29 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Y.182, E:N.188, E:Q.194, E:Q.194 Salt bridges: E:R.200 PQJ.34: 9 residues within 4Å: Chain F: N.176, Q.177, W.179, Y.182, Q.194, M.197, K.198, T.199, R.200 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.200 pi-Cation interactions: F:W.179 PQJ.35: 8 residues within 4Å: Chain E: H.144 Chain F: G.180, P.181, Y.182, N.188, Q.194, R.200 Ligands: SO4.36 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:Y.182, F:N.188, F:Q.194, F:Q.194 Salt bridges: F:R.200 PQJ.40: 8 residues within 4Å: Chain G: N.176, Q.177, W.179, Y.182, Q.194, M.197, T.199, R.200 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:R.200 pi-Cation interactions: G:W.179 PQJ.41: 8 residues within 4Å: Chain G: W.179, G.180, P.181, Y.182, N.188, Q.194, R.200 Ligands: SO4.42 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:Y.182, G:N.188, G:Q.194 Salt bridges: G:R.200

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

SO4.3: 3 residues within 4Å: Chain A: S.186, W.187 Ligands: PQJ.2 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: Y.28, D.29, K.30, E.31 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: Q.64, R.66, R.253 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: Y.65, V.67, P.213 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: R.184, K.271, D.272 Chain B: N.214 Ligand excluded by PLIP SO4.8: 6 residues within 4Å: Chain A: S.106, D.108, K.154 Chain B: A.216, S.217, S.218 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain A: A.216, S.217, S.218 Chain G: D.108, K.154 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: S.186, W.187 Ligands: PQJ.11 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: Y.65, V.67, P.213 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain B: R.184, K.271, D.272 Chain C: N.214 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain C: S.186, W.187 Ligands: PQJ.16 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain C: D.29, K.30, E.31 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain C: Q.64, R.66, R.253 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain C: R.184, D.272 Chain D: N.214 Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Chain B: D.108, K.154 Chain C: A.216, S.217, S.218 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain D: S.186, W.187 Ligands: PQJ.23 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain D: Q.64, R.66, R.253 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain D: R.184, D.272 Chain E: N.214 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain E: S.186, W.187 Ligands: PQJ.28 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain E: D.29, K.30, E.31 Ligand excluded by PLIP SO4.31: 2 residues within 4Å: Chain E: A.62, Q.64 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain E: R.184, D.272 Chain F: N.214 Ligand excluded by PLIP SO4.33: 5 residues within 4Å: Chain E: D.108, K.154 Chain F: A.216, S.217, S.218 Ligand excluded by PLIP SO4.36: 3 residues within 4Å: Chain F: S.186, W.187 Ligands: PQJ.35 Ligand excluded by PLIP SO4.37: 2 residues within 4Å: Chain F: R.66, R.253 Ligand excluded by PLIP SO4.38: 3 residues within 4Å: Chain F: R.184, D.272 Chain G: N.214 Ligand excluded by PLIP SO4.39: 6 residues within 4Å: Chain F: S.106, D.108, K.154 Chain G: A.216, S.217, S.218 Ligand excluded by PLIP SO4.42: 3 residues within 4Å: Chain G: S.186, W.187 Ligands: PQJ.41 Ligand excluded by PLIP SO4.43: 4 residues within 4Å: Chain G: Y.28, D.29, K.30, E.31 Ligand excluded by PLIP SO4.44: 3 residues within 4Å: Chain G: Q.64, R.66, R.253 Ligand excluded by PLIP SO4.45: 3 residues within 4Å: Chain G: Y.65, V.67, P.213 Ligand excluded by PLIP SO4.46: 3 residues within 4Å: Chain A: N.214 Chain G: R.184, D.272 Ligand excluded by PLIP SO4.47: 4 residues within 4Å: Chain A: S.222 Chain G: E.158, S.159, K.168 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

Alpha-hemolysin: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Membrane

We predict this structure to be a membrane protein.
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Alpha-hemolysin

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