SMTL ID : 4kqr.1 (1 other biounit)

CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH (5S)-Penicilloic Acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

monomer

Ligands

1 x VPP: (2S,4S)-2-[(R)-carboxy{[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-2-phenylacetyl]amino}methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid(Non-covalent)

VPP.1: 19 residues within 4Å: Chain A: S.279, K.282, V.318, S.334, N.336, T.389, Y.392, Y.394, S.470, G.471, T.472, A.473, R.474, Y.483, Y.488, F.518, G.519, G.520 Ligands: IMD.9 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:V.318, A:T.389, A:Y.394, A:T.472, A:Y.488 Hydrogen bonds: A:S.279, A:S.279, A:S.334, A:N.336, A:Y.392, A:S.470, A:T.472, A:T.472, A:T.472, A:T.472, A:R.474, A:G.519, A:G.520 Water bridges: A:K.282, A:R.316, A:V.318, A:N.336 Salt bridges: A:K.282, A:K.469

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

CL.2: 4 residues within 4Å: Chain A: R.484, E.485, N.486, A.487 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: V.478, G.479 Ligand excluded by PLIP

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: G.232, S.233, R.269, F.275, R.489, V.508, D.510 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.232, A:S.233, A:R.269, A:R.269, A:R.489 GOL.5: 5 residues within 4Å: Chain A: Y.253, N.254, N.257, R.258, L.261 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.254 GOL.6: 3 residues within 4Å: Chain A: D.413, S.440, Q.443 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.413 GOL.7: 6 residues within 4Å: Chain A: N.486, P.512, S.513, K.514, G.516, Y.517 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.515, A:G.516, A:G.516 GOL.8: 4 residues within 4Å: Chain A: R.458, A.515, L.521, P.525 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.458, A:A.515 Water bridges: A:E.226, A:E.226, A:N.227

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.9: 5 residues within 4Å: Chain A: Y.313, T.314, T.389, Y.392 Ligands: VPP.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.314 IMD.10: 3 residues within 4Å: Chain A: F.167, W.170, L.204 2 PLIP interactions: 2 interactions with chain A pi-Stacking: A:F.167, A:W.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

van Berkel, S.S. et al., Binding of (5S)-Penicilloic Acid to Penicillin Binding Protein 3. Acs Chem.Biol. (2013)

Release Date

2013-11-06

Peptides

Penicillin-binding protein 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Penicillin-binding protein 3

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