SMTL ID : 6l7f.1 (1 other biounit)

Metallo beta-lactamase fold protein (cAMP free)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-trimer

Ligands

6 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 7 residues within 4Å: Chain A: H.69, H.71, H.131, D.165 Ligands: NI.4, ZN.5, ZN.6 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.69, A:H.71, A:H.131, A:D.165, H2O.2 NI.4: 7 residues within 4Å: Chain A: D.73, H.74, D.165, H.216 Ligands: NI.1, ZN.5, ZN.6 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.73, A:H.74, A:D.165, A:H.216, H2O.2, H2O.4 NI.7: 7 residues within 4Å: Chain B: H.69, H.71, H.131, D.165 Ligands: NI.9, ZN.10, ZN.11 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.69, B:H.71, B:H.131, B:D.165, H2O.5 NI.9: 7 residues within 4Å: Chain B: D.73, H.74, D.165, H.216 Ligands: NI.7, ZN.10, ZN.11 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.73, B:H.74, B:D.165, B:H.216, H2O.5 NI.12: 8 residues within 4Å: Chain C: H.69, H.71, H.74, H.131, D.165 Ligands: NI.14, ZN.15, ZN.16 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.69, C:H.71, C:H.131, C:D.165, H2O.8 NI.14: 7 residues within 4Å: Chain C: D.73, H.74, D.165, H.216 Ligands: NI.12, ZN.15, ZN.16 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.73, C:H.74, C:D.165, C:H.216, H2O.8

3 x CS: CESIUM ION(Non-covalent)

CS.2: 4 residues within 4Å: Chain A: I.47, N.50, C.53, L.55 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.53 CS.8: 4 residues within 4Å: Chain B: I.47, N.50, C.53, L.55 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.53 CS.13: 4 residues within 4Å: Chain C: I.47, N.50, C.53, L.55 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:C.53

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 3 residues within 4Å: Chain A: S.170 Chain B: S.170 Chain C: S.170 12 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A, 4 interactions with chain C Hydrogen bonds: B:S.170, B:S.170, B:S.173, B:S.173, A:S.170, A:S.173, A:S.173, C:S.170, C:S.173, C:S.173 Water bridges: A:D.171, C:D.171

6 x ZN: ZINC ION(Non-covalent)

ZN.5: 7 residues within 4Å: Chain A: D.73, H.74, D.165, H.216 Ligands: NI.1, NI.4, ZN.6 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.73, A:H.74, A:D.165, A:H.216, H2O.2, H2O.4 ZN.6: 7 residues within 4Å: Chain A: H.69, H.71, H.131, D.165 Ligands: NI.1, NI.4, ZN.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.69, A:H.71, A:H.131, A:D.165, H2O.2 ZN.10: 8 residues within 4Å: Chain B: H.69, H.71, H.74, H.131, D.165 Ligands: NI.7, NI.9, ZN.11 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.69, B:H.71, B:H.131, B:D.165, H2O.5 ZN.11: 7 residues within 4Å: Chain B: D.73, H.74, D.165, H.216 Ligands: NI.7, NI.9, ZN.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.73, B:H.74, B:D.165, B:H.216, H2O.5 ZN.15: 8 residues within 4Å: Chain C: H.69, H.71, H.74, H.131, D.165 Ligands: NI.12, NI.14, ZN.16 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.69, C:H.71, C:H.131, C:D.165, H2O.8 ZN.16: 7 residues within 4Å: Chain C: D.73, H.74, D.165, H.216 Ligands: NI.12, NI.14, ZN.15 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.73, C:H.74, C:D.165, C:H.216, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, K.-Y. et al., Metallo beta-lactamase fold protein. To Be Published

Release Date

2021-02-03

Peptides

UPF0173 metal-dependent hydrolase C7P97_11315: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

UPF0173 metal-dependent hydrolase C7P97_11315