SMTL ID : 7e3v.1 (1 other biounit)

Metallo beta-lactamase fold protein (cAMP free)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-trimer

Ligands

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

TRS.1: 4 residues within 4Å: Chain A: S.166 Chain B: S.166 Chain C: S.166 Ligands: CL.2 7 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: A:S.166, A:S.166, A:S.166, C:S.166, B:S.166 Water bridges: A:S.166, C:S.166

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

CL.2: 7 residues within 4Å: Chain A: S.166, D.167 Chain B: S.166, D.167 Chain C: S.166, D.167 Ligands: TRS.1 Ligand excluded by PLIP

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

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

6 x ZN: ZINC ION(Non-covalent)

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

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
A

B
B

C
C

UPF0173 metal-dependent hydrolase C7P97_11315

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