SMTL ID : 5fqc.2 (1 other biounit)

Crystal structure of the metallo-beta-lactamase VIM-2 with 2C

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 4 residues within 4Å: Chain A: A.108, H.129 Ligands: FMT.2, ZN.5 No protein-ligand interaction detected (PLIP) FMT.2: 7 residues within 4Å: Chain A: V.107, A.108, T.109, T.128, H.129 Ligands: FMT.1, ZN.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.107, A:T.109 Water bridges: A:T.128

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.90, H.92, H.155 Ligands: OK3.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.90, A:H.92, A:H.155 ZN.4: 5 residues within 4Å: Chain A: D.94, R.95, C.174, H.216 Ligands: OK3.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.94, A:C.174, A:H.216 ZN.5: 3 residues within 4Å: Chain A: H.129 Ligands: FMT.1, FMT.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.129

1 x OK3: (4~{R})-4-[[4-(aminomethyl)phenyl]carbonylamino]-3,3-bis(oxidanyl)-2-oxa-3-boranuidabicyclo[4.4.0]deca-1(10),6,8-triene-10-carboxylic acid(Non-covalent)

OK3.6: 16 residues within 4Å: Chain A: F.38, Y.43, W.63, H.90, H.92, D.93, D.94, E.122, H.155, C.174, G.185, N.186, D.189, H.216 Ligands: ZN.3, ZN.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.38, A:Y.43, A:W.63, A:W.63, A:N.186 Hydrogen bonds: A:D.93, A:E.122, A:N.186, A:N.186, A:N.186 Salt bridges: A:H.155, A:H.216 pi-Stacking: A:F.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brem, J. et al., Structural basis of metallo-beta-lactamase, serine-beta-lactamase and penicillin-binding protein inhibition by cyclic boronates. Nat Commun (2016)

Release Date

2016-08-17

Peptides

BETA-LACTAMASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

BETA-LACTAMASE

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