SMTL ID : 2y2o.1

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (EO9)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

2 x EO9: [(1S)-1-[(2,6-difluorophenyl)carbonylamino]ethyl]-trihydroxy-boron(Covalent)

EO9.1: 12 residues within 4Å: Chain A: A.162, S.163, Y.201, A.202, S.219, N.221, G.356, T.357, T.358, G.359, D.361 Ligands: NA.16 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.357 Hydrogen bonds: A:S.163, A:S.219, A:N.221, A:T.357, A:T.357, A:T.357 Water bridges: A:A.202 EO9.18: 12 residues within 4Å: Chain B: A.162, S.163, Y.201, A.202, S.219, N.221, G.356, T.357, T.358, G.359, D.361 Ligands: NA.33 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:T.357 Hydrogen bonds: B:S.163, B:S.219, B:N.221, B:T.357, B:T.357, B:T.357 Water bridges: B:A.202

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

SO4.2: 4 residues within 4Å: Chain A: K.158, T.266, Q.269, K.286 7 PLIP interactions: 7 interactions with chain A Water bridges: A:K.158, A:K.158, A:K.158, A:Q.269, A:K.286 Salt bridges: A:K.158, A:K.286 SO4.19: 4 residues within 4Å: Chain B: K.158, T.266, Q.269, K.286 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.266 Water bridges: B:K.158, B:K.158, B:K.158, B:Q.269, B:K.286 Salt bridges: B:K.158, B:K.286

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

CL.3: 1 residues within 4Å: Chain A: R.232 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: V.238, K.239 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: S.328, R.330, K.336 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: A.294, A.295, D.296, R.298 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: Y.247, E.248, V.265, Q.269 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: E.49, H.287, V.288, I.289 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain A: D.40, Y.41, L.42, H.102, Q.106 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: S.312, K.313 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: Y.10, D.12, I.97, D.98, Q.99 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: N.462, K.463, S.464 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: H.381, D.382, D.383 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: Y.41, F.44, T.45, N.152 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain A: R.61 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain A: T.334, S.337 Chain B: T.334, S.337 Ligands: CL.34 Ligand excluded by PLIP CL.20: 1 residues within 4Å: Chain B: R.232 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain B: V.238, K.239 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain B: S.328, R.330, K.336 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain B: A.294, A.295, D.296, R.298 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain B: Y.247, E.248, V.265, Q.269 Ligand excluded by PLIP CL.25: 4 residues within 4Å: Chain B: E.49, H.287, V.288, I.289 Ligand excluded by PLIP CL.26: 5 residues within 4Å: Chain B: D.40, Y.41, L.42, H.102, Q.106 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain B: S.312, K.313 Ligand excluded by PLIP CL.28: 5 residues within 4Å: Chain B: Y.10, D.12, I.97, D.98, Q.99 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain B: N.462, K.463, S.464 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain B: H.381, D.382, D.383 Ligand excluded by PLIP CL.31: 4 residues within 4Å: Chain B: Y.41, F.44, T.45, N.152 Ligand excluded by PLIP CL.32: 1 residues within 4Å: Chain B: R.61 Ligand excluded by PLIP CL.34: 5 residues within 4Å: Chain A: T.334, S.337 Chain B: T.334, S.337 Ligands: CL.17 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.16: 4 residues within 4Å: Chain A: T.355, G.356, T.357 Ligands: EO9.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.355, A:T.357 Water bridges: A:T.355 NA.33: 4 residues within 4Å: Chain B: T.355, G.356, T.357 Ligands: EO9.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.355, B:T.355

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Contreras-Martel, C. et al., Structure-Guided Design of Cell Wall Biosynthesis Inhibitors that Overcome Beta-Lactam Resistance in Staphylococcus Aureus (Mrsa). Acs Chem.Biol. (2011)

Release Date

2011-08-03

Peptides

PENICILLIN-BINDING PROTEIN 1B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

PENICILLIN-BINDING PROTEIN 1B

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