SMTL ID : 6u49.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-heptamer

Ligands

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

PQJ.1: 8 residues within 4Å: Chain A: N.176, Q.177, W.179, Y.182, Q.194, M.197, K.198, R.200 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.200 Salt bridges: A:R.200 PQJ.2: 5 residues within 4Å: Chain A: W.179, G.180, P.181, Y.182 Ligands: PQJ.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.180, A:Y.182, A:Y.182 PQJ.3: 8 residues within 4Å: Chain A: Y.112, S.114, G.143, H.144 Chain C: N.178, W.179 Chain G: L.116, Y.118 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Water bridges: A:Y.112 Salt bridges: A:H.144 pi-Cation interactions: C:W.179, C:W.179 PQJ.4: 9 residues within 4Å: Chain B: 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 B Hydrogen bonds: B:R.200 pi-Cation interactions: B:W.179 PQJ.5: 7 residues within 4Å: Chain B: W.179, G.180, P.181, Y.182, Q.194, R.200 Ligands: SO4.7 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.180, B:G.180, B:Y.182, B:R.200 Water bridges: B:N.188, B:N.188, B:Q.194 PQJ.6: 10 residues within 4Å: Chain B: N.178, W.179 Chain F: L.116, Y.118 Chain G: Y.112, S.114, I.142, G.143, H.144 Ligands: PQJ.2 4 PLIP interactions: 1 interactions with chain G, 3 interactions with chain B Salt bridges: G:H.144 Water bridges: B:N.178 pi-Cation interactions: B:W.179, B:W.179 PQJ.8: 9 residues within 4Å: Chain C: N.176, Q.177, W.179, Y.182, Q.194, M.197, K.198, T.199, R.200 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.200 PQJ.9: 7 residues within 4Å: Chain C: G.180, P.181, Y.182, N.188, Q.194, R.200 Ligands: SO4.10 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.188, C:Q.194 Water bridges: C:Y.182 Salt bridges: C:R.200 PQJ.11: 7 residues within 4Å: Chain D: N.176, Q.177, W.179, Y.182, Q.194, M.197, R.200 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.200 Salt bridges: D:R.200 PQJ.12: 6 residues within 4Å: Chain D: W.179, G.180, P.181, Y.182, R.200 Ligands: SO4.14 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:G.180, D:G.180, D:R.200 Water bridges: D:Q.194, B:Y.118 PQJ.13: 8 residues within 4Å: Chain A: Y.118 Chain B: Y.112, S.114, I.142, G.143, H.144 Chain D: N.178, W.179 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B pi-Cation interactions: D:W.179, D:W.179 Water bridges: B:Y.112 Salt bridges: B:H.144 PQJ.15: 8 residues within 4Å: Chain E: N.176, Q.177, W.179, Y.182, Q.194, M.197, K.198, R.200 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.200 PQJ.16: 7 residues within 4Å: Chain E: W.179, G.180, P.181, Y.182, Q.194, R.200 Ligands: SO4.19 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:G.180, E:Y.182, E:R.200 PQJ.17: 9 residues within 4Å: Chain B: L.116, Y.118 Chain C: Y.112, S.114, I.142, G.143, H.144 Chain E: N.178, W.179 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain E Hydrogen bonds: C:Y.112 Water bridges: C:Y.112, C:H.144 Salt bridges: C:H.144 pi-Cation interactions: E:W.179, E:W.179 PQJ.18: 7 residues within 4Å: Chain D: Y.118 Chain E: Y.112, S.114, G.143, H.144 Chain G: N.178, W.179 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain E pi-Cation interactions: G:W.179, G:W.179 Salt bridges: E:H.144 PQJ.20: 9 residues within 4Å: Chain A: N.178, W.179 Chain E: L.116, Y.118 Chain F: Y.112, S.114, I.142, G.143, H.144 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:Y.112 Water bridges: F:H.144, F:H.144 Salt bridges: F:H.144 pi-Cation interactions: A:W.179, A:W.179 PQJ.21: 8 residues within 4Å: Chain F: N.176, Q.177, W.179, Y.182, Q.194, M.197, K.198, R.200 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:R.200 PQJ.22: 4 residues within 4Å: Chain F: W.179, G.180, P.181, Y.182 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:G.180, F:G.180, F:Y.182 PQJ.23: 9 residues within 4Å: Chain C: L.116, Y.118 Chain D: Y.112, S.114, I.142, G.143, H.144 Chain F: N.178, W.179 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain F Hydrogen bonds: D:Y.112 Water bridges: D:H.144, D:H.144 Salt bridges: D:H.144 pi-Cation interactions: F:W.179, F:W.179 PQJ.24: 8 residues within 4Å: Chain G: N.176, Q.177, W.179, Y.182, Q.194, M.197, T.199, R.200 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:R.200 PQJ.25: 7 residues within 4Å: Chain G: W.179, G.180, P.181, Y.182, N.188, Q.194 Ligands: SO4.26 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Y.182, G:N.188

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

SO4.7: 3 residues within 4Å: Chain B: S.186, W.187 Ligands: PQJ.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.187 Water bridges: B:D.185, B:S.186 SO4.10: 3 residues within 4Å: Chain C: S.186, W.187 Ligands: PQJ.9 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:W.187, C:W.187 SO4.14: 3 residues within 4Å: Chain D: S.186, W.187 Ligands: PQJ.12 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:W.187, D:W.187 SO4.19: 3 residues within 4Å: Chain E: S.186, W.187 Ligands: PQJ.16 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:W.187 SO4.26: 3 residues within 4Å: Chain G: S.186, W.187 Ligands: PQJ.25 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:W.187, G:W.187

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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