SMTL ID : 7zuk.1

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with lactone 7Az - Streptococcus pneumoniae R6

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

monomer

Ligands

1 x KQI: 6-azido-N-[(2S)-1-oxidanylidene-1-[[(2S,3R)-3-oxidanyl-1-oxidanylidene-butan-2-yl]amino]-3-phenyl-propan-2-yl]hexanamide(Covalent)

KQI.1: 13 residues within 4Å: Chain A: S.457, A.459, S.460, M.497, S.516, N.518, M.556, G.557, G.653, T.654, T.655, G.656 Ligands: CL.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:M.497, A:M.556, A:T.655 Hydrogen bonds: A:S.460, A:N.518, A:T.654, A:T.654

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

CL.2: 4 residues within 4Å: Chain A: T.652, G.653, T.654 Ligands: KQI.1 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: V.533, V.535, K.536 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: R.456, S.457, E.561, N.660 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: I.772, G.773 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: V.724, K.725 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: N.759, K.760, S.761 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: I.394, D.395, Q.396 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: S.726, E.727, K.735 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: A.591, A.592, D.593, R.595 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain A: R.529 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: Y.544, E.545, V.562, Q.566 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain A: E.346, H.584, V.585, I.586 Ligands: DMS.25 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain A: D.337, Y.338, L.339, H.399, Q.403 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: S.609, K.610 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain A: T.631, S.634 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain A: E.511, N.514, Y.515 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain A: S.775, D.776, A.777 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain A: T.642, N.645 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain A: Y.338, F.341, T.342, N.449 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain A: D.679, D.680 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain A: S.625, R.627, K.633 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain A: A.718, L.719 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain A: T.488, N.489 Ligand excluded by PLIP

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.25: 6 residues within 4Å: Chain A: E.346, F.452, K.583, H.584, V.585 Ligands: CL.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.583 Salt bridges: A:E.346

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Flanders, P.L. et al., Combined Structural Analysis and Molecular Dynamics Reveal Penicillin-Binding Protein Inhibition Mode with beta-Lactones. Acs Chem.Biol. (2022)

Release Date

2022-11-02

Peptides

Penicillin-binding protein 1b: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Penicillin-binding protein 1b

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