SMTL ID : 2y2p.1

Penicillin-binding protein 1b (pbp-1b) in complex with an alkyl boronate (z10)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-dimer

Ligands

2 x Z10: [(1S)-1-[(2-fluoro-6-phenyl-phenyl)carbonylamino]ethyl]-trihydroxy-boron(Covalent)

Z10.1: 14 residues within 4Å: Chain A: A.162, S.163, K.166, Y.201, A.202, S.219, N.221, M.259, G.356, T.357, T.358, G.359, D.361 Ligands: NA.21 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.201, A:M.259, A:T.357 Hydrogen bonds: A:S.163, A:S.219, A:N.221, A:T.357, A:T.357, A:T.357 Z10.23: 14 residues within 4Å: Chain B: A.162, S.163, K.166, Y.201, A.202, S.219, N.221, M.259, G.356, T.357, T.358, G.359, D.361 Ligands: NA.43 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.201, B:M.259, B:T.357 Hydrogen bonds: B:S.163, B:S.219, B:N.221, B:T.357, B:T.357, B:T.357

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

CL.2: 1 residues within 4Å: Chain A: R.232 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: V.236, V.238, K.239 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: S.328, R.330, K.336 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: A.294, A.295, D.296, R.298 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: S.429, E.430, K.438 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: 5 residues within 4Å: Chain A: E.49, R.53, 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: 6 residues within 4Å: Chain A: Y.10, S.11, 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: S.478, D.479, A.480 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: A.421, L.422 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain A: Y.41, F.44, T.45, N.152 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain A: R.61 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain A: H.381, D.382, D.383 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain A: I.254, S.256 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain A: T.191, N.192 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain A: I.475, G.476 Ligand excluded by PLIP CL.22: 5 residues within 4Å: Chain A: T.334, S.337 Chain B: T.334, S.337 Ligands: CL.44 Ligand excluded by PLIP CL.24: 1 residues within 4Å: Chain B: R.232 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain B: V.236, V.238, K.239 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain B: S.328, R.330, K.336 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain B: A.294, A.295, D.296, R.298 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain B: S.429, E.430, K.438 Ligand excluded by PLIP CL.29: 4 residues within 4Å: Chain B: Y.247, E.248, V.265, Q.269 Ligand excluded by PLIP CL.30: 5 residues within 4Å: Chain B: E.49, R.53, H.287, V.288, I.289 Ligand excluded by PLIP CL.31: 5 residues within 4Å: Chain B: D.40, Y.41, L.42, H.102, Q.106 Ligand excluded by PLIP CL.32: 2 residues within 4Å: Chain B: S.312, K.313 Ligand excluded by PLIP CL.33: 6 residues within 4Å: Chain B: Y.10, S.11, D.12, I.97, D.98, Q.99 Ligand excluded by PLIP CL.34: 3 residues within 4Å: Chain B: N.462, K.463, S.464 Ligand excluded by PLIP CL.35: 3 residues within 4Å: Chain B: S.478, D.479, A.480 Ligand excluded by PLIP CL.36: 2 residues within 4Å: Chain B: A.421, L.422 Ligand excluded by PLIP CL.37: 4 residues within 4Å: Chain B: Y.41, F.44, T.45, N.152 Ligand excluded by PLIP CL.38: 1 residues within 4Å: Chain B: R.61 Ligand excluded by PLIP CL.39: 3 residues within 4Å: Chain B: H.381, D.382, D.383 Ligand excluded by PLIP CL.40: 2 residues within 4Å: Chain B: I.254, S.256 Ligand excluded by PLIP CL.41: 2 residues within 4Å: Chain B: T.191, N.192 Ligand excluded by PLIP CL.42: 2 residues within 4Å: Chain B: I.475, G.476 Ligand excluded by PLIP CL.44: 5 residues within 4Å: Chain A: T.334, S.337 Chain B: T.334, S.337 Ligands: CL.22 Ligand excluded by PLIP

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

NA.21: 4 residues within 4Å: Chain A: T.355, G.356, T.357 Ligands: Z10.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.355 Water bridges: A:T.355 NA.43: 4 residues within 4Å: Chain B: T.355, G.356, T.357 Ligands: Z10.23 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.355, B:T.355, B:T.357

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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