SMTL ID : 7uhq.1

Time-Resolved Structure of Metallo Beta-Lactamase L1 in a Complex with Cleaved Moxalactam (4000 ms Snapshot)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: H.90, H.92, D.94, H.95, H.166 Ligands: ZN.2, XQP.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.90, A:H.92, A:H.166 ZN.2: 5 residues within 4Å: Chain A: D.94, H.95, H.231 Ligands: ZN.1, XQP.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.94, A:H.95, A:H.231 ZN.4: 7 residues within 4Å: Chain B: H.90, H.92, D.94, H.95, H.166 Ligands: ZN.5, XQP.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.90, B:H.92, B:H.166 ZN.5: 5 residues within 4Å: Chain B: D.94, H.95, H.231 Ligands: ZN.4, XQP.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.94, B:H.95, B:H.231 ZN.7: 7 residues within 4Å: Chain C: H.90, H.92, D.94, H.95, H.166 Ligands: ZN.8, XQP.9 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.90, C:H.92, C:H.166 ZN.8: 5 residues within 4Å: Chain C: D.94, H.95, H.231 Ligands: ZN.7, XQP.9 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.94, C:H.95, C:H.231 ZN.10: 7 residues within 4Å: Chain D: H.90, H.92, D.94, H.95, H.166 Ligands: ZN.11, XQP.12 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.90, D:H.92, D:H.166 ZN.11: 5 residues within 4Å: Chain D: D.94, H.95, H.231 Ligands: ZN.10, XQP.12 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.94, D:H.95, D:H.231

4 x XQP: (2R)-2-[(R)-carboxy{[(2R)-2-carboxy-2-(4-hydroxyphenyl)acetyl]amino}methoxymethyl]-5-{[(1-methyl-1H-tetrazol-5-yl)sulfanyl]methyl}-3,6-dihydro-2H-1,3-oxazine-4-carboxylic acid(Non-covalent)

XQP.3: 15 residues within 4Å: Chain A: Y.17, W.23, H.90, H.92, D.94, H.95, F.130, I.134, H.166, S.191, S.193, P.195, H.231 Ligands: ZN.1, ZN.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.17, A:P.195 Hydrogen bonds: A:S.191, A:S.193 Salt bridges: A:H.90, A:H.92, A:H.95, A:H.166, A:H.166, A:H.231 XQP.6: 15 residues within 4Å: Chain B: Y.17, W.23, H.90, H.92, D.94, H.95, F.130, I.134, H.166, S.191, S.193, P.195, H.231 Ligands: ZN.4, ZN.5 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.17, B:P.195 Hydrogen bonds: B:S.191, B:S.193 Salt bridges: B:H.90, B:H.92, B:H.95, B:H.166, B:H.166, B:H.231 XQP.9: 15 residues within 4Å: Chain C: Y.17, W.23, H.90, H.92, D.94, H.95, F.130, I.134, H.166, S.191, S.193, P.195, H.231 Ligands: ZN.7, ZN.8 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:Y.17, C:P.195 Hydrogen bonds: C:Y.17, C:S.191, C:S.193 Salt bridges: C:H.90, C:H.92, C:H.95, C:H.166, C:H.166, C:H.231 XQP.12: 15 residues within 4Å: Chain D: Y.17, W.23, H.90, H.92, D.94, H.95, F.130, I.134, H.166, S.191, S.193, P.195, H.231 Ligands: ZN.10, ZN.11 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:Y.17, D:P.195 Hydrogen bonds: D:Y.17, D:S.191, D:S.193 Salt bridges: D:H.90, D:H.92, D:H.95, D:H.166, D:H.166, D:H.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wilamowski, M. et al., Time-resolved beta-lactam cleavage by L1 metallo-beta-lactamase. Nat Commun (2022)

Release Date

2022-04-13

Peptides

Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)

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