SMTL ID : 4hbu.1

Crystal structure of CTX-M-15 extended-spectrum beta-lactamase in complex with avibactam (NXL104)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

monomer

Ligands

1 x NXL: (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide(Covalent)

NXL.1: 13 residues within 4Å: Chain A: C.44, S.45, K.48, N.79, Y.80, S.105, N.107, N.145, T.191, K.209, T.210, G.211, S.212 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.45, A:N.79, A:S.105, A:S.105, A:N.107, A:T.210, A:S.212, A:S.212 Water bridges: A:N.145 Salt bridges: A:K.209

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: K.58, E.62, L.65, Q.68, H.116 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.58, A:E.62 Water bridges: A:H.116 EDO.3: 4 residues within 4Å: Chain A: E.13, G.18, R.19, R.36 No protein-ligand interaction detected (PLIP) EDO.4: 4 residues within 4Å: Chain A: N.26, A.28, D.29, L.263 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.26, A:N.26 EDO.5: 4 residues within 4Å: Chain A: A.54, K.58, V.117, F.126 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.122, A:S.122, A:Q.129 EDO.6: 2 residues within 4Å: Chain A: R.166, L.170 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.166, A:R.166 EDO.7: 5 residues within 4Å: Chain A: I.25, N.30, Q.32, Q.163, R.166 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.163, A:R.166, A:R.166 Water bridges: A:N.30, A:N.30 EDO.8: 4 residues within 4Å: Chain A: R.69, H.87, T.91, E.96 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.69, A:R.69, A:T.91 EDO.9: 7 residues within 4Å: Chain A: R.40, A.42, A.147, I.148, G.150, D.151, T.155 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.147, A:G.150 Water bridges: A:R.40, A:A.147, A:G.150 EDO.10: 3 residues within 4Å: Chain A: Q.103, T.184, W.185 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.103 EDO.11: 2 residues within 4Å: Chain A: S.75, D.76 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.75 Water bridges: A:D.76, A:D.76, A:K.112

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

CL.12: 2 residues within 4Å: Chain A: P.201, A.202 Ligand excluded by PLIP

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

SO4.13: 1 residues within 4Å: Chain A: R.128 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.128 Salt bridges: A:R.128 SO4.14: 3 residues within 4Å: Chain A: R.139, T.143, R.153 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.153, A:R.153, A:R.153 Salt bridges: A:R.139, A:R.153 SO4.15: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.179 SO4.16: 1 residues within 4Å: Chain A: R.36 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lahiri, S.D. et al., Structural insight into potent broad-spectrum inhibition with reversible recyclization mechanism: avibactam in complex with CTX-M-15 and Pseudomonas aeruginosa AmpC beta-lactamases. Antimicrob.Agents Chemother. (2013)

Release Date

2013-04-10

Peptides

Beta-lactamase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-lactamase

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