SMTL ID : 2x8m.1

Crystal Structure of CbpF in complex with ipratropium by soaking

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: Y.244, R.246, S.247 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.244, A:Y.244, A:R.246, A:S.247

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: Y.203, G.205, S.206, S.207, K.215 Ligands: GOL.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.206, A:S.207, A:S.207, A:K.215 Water bridges: A:Y.203, A:S.209 GOL.4: 3 residues within 4Å: Chain A: G.55, Y.56, N.67 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.67 Water bridges: A:P.65 GOL.6: 7 residues within 4Å: Chain A: F.204, G.205, S.207, S.209, A.211, K.215 Ligands: GOL.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:F.204, A:S.209, A:K.215 Water bridges: A:S.209, A:S.209, A:T.212, A:T.212 GOL.8: 2 residues within 4Å: Chain A: Y.216, W.221 No protein-ligand interaction detected (PLIP) GOL.9: 10 residues within 4Å: Chain A: Y.48, Q.72, E.73, K.142, L.143, Y.151, I.156, V.169, T.170, I.171 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.48, A:Q.72, A:Y.151, A:Y.151 Water bridges: A:K.74 GOL.10: 4 residues within 4Å: Chain A: Q.257, W.262, Y.305, N.306 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.257, A:W.262

3 x X8M: IPRATROPIUM(Non-covalent)

X8M.3: 7 residues within 4Å: Chain A: W.163, W.181, N.198, Y.202, M.210, K.227, N.228 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.163, A:W.163, A:W.163, A:W.181 Hydrogen bonds: A:N.198 Water bridges: A:Y.202 pi-Stacking: A:W.163 pi-Cation interactions: A:W.163, A:W.163, A:W.181, A:W.181 X8M.5: 4 residues within 4Å: Chain A: W.276, W.283, Y.301, W.309 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.276, A:W.276, A:W.283, A:W.283, A:Y.301, A:Y.301, A:W.309, A:W.309 Water bridges: A:W.276 pi-Cation interactions: A:W.276, A:W.276, A:W.283, A:W.283, A:W.309 X8M.7: 10 residues within 4Å: Chain A: F.7, K.14, I.29, D.30, G.31, K.32, Y.34, M.42, D.81, G.82 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.7, A:F.7, A:K.14, A:K.32, A:K.32, A:K.32, A:Y.34 Hydrogen bonds: A:K.32 pi-Cation interactions: A:F.7

6 x CHT: CHOLINE ION(Non-covalent)

CHT.11: 5 residues within 4Å: Chain A: W.194, W.201, Y.222, M.231, S.248 5 PLIP interactions: 5 interactions with chain A Water bridges: A:S.248 pi-Cation interactions: A:W.194, A:W.194, A:W.201, A:W.201 CHT.12: 5 residues within 4Å: Chain A: W.255, W.262, Y.284, L.292, N.306 4 PLIP interactions: 4 interactions with chain A pi-Cation interactions: A:W.255, A:W.255, A:W.262, A:W.262 CHT.13: 6 residues within 4Å: Chain A: W.214, W.221, Y.243, M.251, G.268, N.269 5 PLIP interactions: 5 interactions with chain A Water bridges: A:G.268 pi-Cation interactions: A:W.214, A:W.214, A:W.221, A:W.221 CHT.14: 5 residues within 4Å: Chain A: W.235, W.242, Y.263, M.272, S.289 4 PLIP interactions: 4 interactions with chain A pi-Cation interactions: A:W.235, A:W.235, A:W.242, A:W.242 CHT.15: 5 residues within 4Å: Chain A: W.130, W.137, Y.182, M.190, S.207 6 PLIP interactions: 6 interactions with chain A Water bridges: A:D.166, A:Y.182, A:Y.182 pi-Cation interactions: A:W.130, A:W.137, A:W.137 CHT.16: 5 residues within 4Å: Chain A: T.117, Y.119, E.133, Y.138, V.159 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:E.133 pi-Cation interactions: A:Y.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martin, N.S. et al., Crystal Structures of Cbpf Complexed with Atropine and Ipratropium Reveal Clues for the Design of Novel Antimicrobials Against Streptococcus Pneumoniae. Biochim.Biophys.Acta (2013)

Release Date

2011-04-06

Peptides

CHOLINE-BINDING PROTEIN F: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CHOLINE-BINDING PROTEIN F

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