SMTL ID : 5a92.1

15K X-ray structure with Cefotaxime: Exploring the Mechanism of beta- Lactam Ring Protonation in the Class A beta-lactamase Acylation Mechanism Using Neutron and X-ray Crystallography

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

monomer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: W.203, P.225, E.226, N.227, H.228, F.262 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.226, A:N.227, A:N.227 Water bridges: A:W.203, A:F.262 Salt bridges: A:H.228 SO4.2: 4 residues within 4Å: Chain A: N.246, R.247, N.248, D.249 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.248, A:N.248, A:D.249, A:D.249 Water bridges: A:N.246, A:D.249 SO4.3: 1 residues within 4Å: Chain A: R.152 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.138 Water bridges: A:R.152, A:R.152 Salt bridges: A:R.152 SO4.4: 3 residues within 4Å: Chain A: K.62, H.63, N.66 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.66 Water bridges: A:N.66 Salt bridges: A:H.63 SO4.6: 3 residues within 4Å: Chain A: P.200, K.201, S.202 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.201, A:S.202, A:S.202

1 x CEF: CEFOTAXIME, C3' cleaved, open, bound form(Covalent)

CEF.5: 16 residues within 4Å: Chain A: C.43, S.44, N.78, Y.79, S.104, N.106, P.141, T.142, N.144, K.208, T.209, G.210, S.211, G.212, D.213, N.246 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.44, A:N.78, A:S.104, A:S.104, A:N.106, A:P.141, A:N.144, A:T.209, A:S.211, A:S.211 Water bridges: A:S.211 Salt bridges: A:K.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vandavasi, V.G. et al., Exploring the Mechanism of Beta-Lactam Ring Protonation in the Class a Beta-Lactamase Acylation Mechanism Using Neutron and X-Ray Crystallography. J.Med.Chem. (2016)

Release Date

2015-12-16

Peptides

BETA-LACTAMASE CTX-M-97: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

BETA-LACTAMASE CTX-M-97

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