SMTL ID : 8gcx.1

XFEL structure of Mycobacterium tuberculosis beta lactamase microcrystals mixed with sulbactam for 700 ms

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-tetramer

Ligands

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 11 residues within 4Å: Chain A: S.44, S.102, T.192, R.196, K.210, T.211, G.212, T.213 Chain B: Q.82, Q.83 Ligands: TSL.2 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.196, A:T.211, A:T.211, A:T.213, A:T.213, B:Q.82, B:Q.83, B:Q.83 Salt bridges: A:K.210 PO4.3: 8 residues within 4Å: Chain B: S.44, S.102, T.192, K.210, T.211, G.212, T.213 Ligands: TSL.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.44, B:S.44, B:S.102, B:T.192, B:T.211, B:T.213, B:T.213, B:T.213 Salt bridges: B:K.210 PO4.5: 11 residues within 4Å: Chain C: S.44, S.102, T.192, R.196, K.210, T.211, G.212, T.213 Chain D: Q.82, Q.83 Ligands: TSL.6 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.44, C:S.102, C:S.102, C:T.211, C:T.213, D:Q.83 Salt bridges: C:K.210 PO4.7: 9 residues within 4Å: Chain D: S.44, S.102, T.192, R.196, K.210, T.211, G.212, T.213 Ligands: TSL.8 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.44, D:S.102, D:T.211, D:T.211, D:T.213 Salt bridges: D:K.210

4 x TSL: TRANS-ENAMINE INTERMEDIATE OF SULBACTAM(Covalent)

TSL.2: 19 residues within 4Å: Chain A: C.43, S.44, K.47, S.76, I.77, S.102, E.142, P.143, N.146, R.147, K.210, G.212, T.213, G.214, D.215 Chain B: S.71, V.85, Q.86 Ligands: PO4.1 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.47, A:S.102, A:P.143, B:Q.86, B:Q.86 Hydrophobic interactions: B:V.85 TSL.4: 16 residues within 4Å: Chain A: Q.83 Chain B: C.43, S.44, K.47, S.76, I.77, S.102, E.142, P.143, N.146, R.147, K.210, G.212, T.213, G.214 Ligands: PO4.3 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:N.146 Hydrogen bonds: B:S.44, B:N.146, B:T.213, A:Q.83 TSL.6: 18 residues within 4Å: Chain C: C.43, S.44, K.47, S.76, I.77, S.102, E.142, P.143, N.146, R.147, K.210, T.213, G.214, D.215 Chain D: S.71, V.85, Q.86 Ligands: PO4.5 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:I.77, D:V.85 Hydrogen bonds: C:S.44, C:K.47, C:S.102, C:P.143, D:Q.86 Salt bridges: C:E.142 TSL.8: 15 residues within 4Å: Chain C: Q.83 Chain D: C.43, S.44, K.47, S.76, I.77, S.102, E.142, P.143, L.145, N.146, R.147, T.213, G.214 Ligands: PO4.7 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:P.143, D:N.146 Hydrogen bonds: D:N.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malla, T.N. et al., Heterogeneity in M. tuberculosis beta-lactamase inhibition by Sulbactam. Nat Commun (2023)

Release Date

2023-09-20

Peptides

Beta-lactamase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Beta-lactamase

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