SMTL ID : 9flj.1

Crystal structure of the C-terminal domain of VldE from Streptococcus pneumoniae containing three zinc atoms at the binding site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

ACT.1: 2 residues within 4Å: Chain A: E.28 Ligands: CD.6 No protein-ligand interaction detected (PLIP)

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: H.50, D.57, E.117, H.122, H.124 Ligands: ZN.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.50, A:D.57, A:D.57, A:E.117, A:H.124 ZN.3: 4 residues within 4Å: Chain A: D.57, E.117, H.122 Ligands: ZN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.57, A:E.117, A:E.117, A:H.122, H2O.1 ZN.4: 3 residues within 4Å: Chain A: H.119, D.121, H.122 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.121, A:H.122, H2O.1, H2O.1, H2O.2 ZN.5: 1 residues within 4Å: Chain A: G.129 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:G.129

1 x CD: CADMIUM ION(Non-covalent)

CD.6: 2 residues within 4Å: Chain A: E.28 Ligands: ACT.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.28, A:E.28, ACT.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miguel-Ruano, V. et al., Characterization of VldE (Spr1875), a Pneumococcal Two-State l,d-Endopeptidase with a Four-Zinc Cluster in the Active Site. Acs Catalysis (2024)

Release Date

2025-01-22

Peptides

LysM domain-containing protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AA

LysM domain-containing protein

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