SMTL ID : 7e3w.2 (1 other biounit)

Metallo beta-lactamase fold protein (cAMP bound)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-trimer

Ligands

3 x CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE(Non-covalent)

CMP.1: 4 residues within 4Å: Chain A: F.68, F.188, F.216, L.218 2 PLIP interactions: 2 interactions with chain A pi-Stacking: A:F.68, A:F.68 CMP.8: 4 residues within 4Å: Chain B: F.68, F.188, F.216, L.218 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.218 Water bridges: B:F.68, B:T.132 pi-Stacking: B:F.68, B:F.68 CMP.13: 4 residues within 4Å: Chain C: F.68, F.188, F.216, L.218 2 PLIP interactions: 2 interactions with chain C pi-Stacking: C:F.68, C:F.68

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

TRS.2: 4 residues within 4Å: Chain A: S.166 Chain B: S.166 Chain C: S.166 Ligands: CL.3 10 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B, 4 interactions with chain C Hydrogen bonds: A:S.166, A:S.169, A:S.169, B:S.166, B:S.169, B:S.169, C:S.166, C:S.166, C:S.169, C:S.169

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

CL.3: 7 residues within 4Å: Chain A: S.166, D.167 Chain B: S.166, D.167 Chain C: S.166, D.167 Ligands: TRS.2 Ligand excluded by PLIP

6 x ZN: ZINC ION(Non-covalent)

ZN.4: 7 residues within 4Å: Chain A: D.69, H.70, D.161, H.212 Ligands: ZN.5, NI.6, NI.7 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.69, A:H.70, A:D.161, H2O.1, H2O.5 ZN.5: 7 residues within 4Å: Chain A: H.65, H.67, H.127, D.161 Ligands: ZN.4, NI.6, NI.7 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.65, A:H.67, A:H.127, A:D.161, H2O.5 ZN.9: 7 residues within 4Å: Chain B: D.69, H.70, D.161, H.212 Ligands: ZN.10, NI.11, NI.12 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.69, B:H.70, B:D.161, H2O.6, H2O.9 ZN.10: 7 residues within 4Å: Chain B: H.65, H.67, H.127, D.161 Ligands: ZN.9, NI.11, NI.12 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.65, B:H.67, B:H.127, B:D.161, H2O.9 ZN.14: 8 residues within 4Å: Chain C: Q.25, D.69, H.70, D.161, H.212 Ligands: ZN.15, NI.16, NI.17 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.69, C:H.70, C:D.161, H2O.12, H2O.14 ZN.15: 8 residues within 4Å: Chain C: H.65, H.67, H.70, H.127, D.161 Ligands: ZN.14, NI.16, NI.17 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.65, C:H.67, C:H.127, C:D.161, H2O.13

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

NI.6: 7 residues within 4Å: Chain A: D.69, H.70, D.161, H.212 Ligands: ZN.4, ZN.5, NI.7 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.69, A:H.70, A:D.161, H2O.1, H2O.5 NI.7: 7 residues within 4Å: Chain A: H.65, H.67, H.127, D.161 Ligands: ZN.4, ZN.5, NI.6 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.65, A:H.67, A:H.127, A:D.161, H2O.5 NI.11: 7 residues within 4Å: Chain B: D.69, H.70, D.161, H.212 Ligands: ZN.9, ZN.10, NI.12 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.69, B:H.70, B:D.161, H2O.6, H2O.9 NI.12: 7 residues within 4Å: Chain B: H.65, H.67, H.127, D.161 Ligands: ZN.9, ZN.10, NI.11 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.65, B:H.67, B:H.127, B:D.161, H2O.9 NI.16: 8 residues within 4Å: Chain C: Q.25, D.69, H.70, D.161, H.212 Ligands: ZN.14, ZN.15, NI.17 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.69, C:H.70, C:D.161, H2O.12, H2O.14 NI.17: 8 residues within 4Å: Chain C: H.65, H.67, H.70, H.127, D.161 Ligands: ZN.14, ZN.15, NI.16 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.65, C:H.67, C:H.127, C:D.161, H2O.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, D.G. et al., Structural and functional studies of SAV1707 from Staphylococcus aureus elucidate its distinct metal-dependent activity and a crucial residue for catalysis. Acta Crystallogr D Struct Biol (2021)

Release Date

2022-02-23

Peptides

UPF0173 metal-dependent hydrolase C7P97_11315: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

UPF0173 metal-dependent hydrolase C7P97_11315

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