SMTL ID : 8ztb.1

Crystal Structure of Active Site Influencing Variant (F218Y) of Imp-1 Metallo-beta-lactamase.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 8 residues within 4Å: Chain A: T.82, G.83, I.85, E.86, L.105, K.110, V.111 Ligands: ACT.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.110 Hydrogen bonds: A:T.82, A:T.82, A:I.85, A:E.86, A:E.86 ACT.2: 7 residues within 4Å: Chain A: A.52, G.83, G.84, I.85, E.86, W.87 Ligands: ACT.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.86 Hydrogen bonds: A:G.83, A:W.87

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: D.80, C.157, K.160, H.196 Ligands: ZN.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.80, A:C.157, A:H.196 ZN.4: 5 residues within 4Å: Chain A: H.76, H.78, H.138, C.157 Ligands: ZN.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.78 ZN.12: 6 residues within 4Å: Chain B: H.76, H.78, D.80, H.138, C.157 Ligands: ZN.13 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.76, B:H.78, B:H.138, B:H.138 ZN.13: 5 residues within 4Å: Chain B: D.80, C.157, K.160, H.196 Ligands: ZN.12 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.80, B:C.157, B:H.196

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 7 residues within 4Å: Chain A: S.75, N.142, V.143, G.155, G.156, C.157, F.158 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.75, A:C.157, A:F.158

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

CL.6: 5 residues within 4Å: Chain A: S.98, L.100, Y.133, D.141, V.143 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: E.86, N.89, S.90 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain A: S.74, S.75, A.97, S.98, T.101, V.143 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: E.198 Chain B: H.33 Ligand excluded by PLIP

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 3 residues within 4Å: Chain B: W.27, V.30, H.196 No protein-ligand interaction detected (PLIP) PEG.11: 4 residues within 4Å: Chain B: S.98, S.118, G.119, Y.133 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.98, B:S.98, B:G.119

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

PO4.14: 6 residues within 4Å: Chain B: T.82, I.85, E.86, L.105, K.110, V.111 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.82, B:T.82, B:T.82, B:I.85, B:E.86, B:E.86, B:E.86, B:V.111 PO4.15: 5 residues within 4Å: Chain B: V.120, Y.133, P.134, G.135, L.181 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.134

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

SO4.16: 4 residues within 4Å: Chain B: L.100, E.103, L.104, P.140 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.104, B:D.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baidya, S. et al., Crystal Structure of Active Site Influencing Variant (F218Y) of Imp-1 Metallo-beta-lactamase. To Be Published

Release Date

2025-06-11

Peptides

Metallo-beta-lactamase type 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Metallo-beta-lactamase type 2