SMTL ID : 4q6p.1

Structural analysis of the Zn-form I of Helicobacter pylori Csd4, a D,L-carboxypeptidase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

monomer

Ligands

8 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.1: 4 residues within 4Å: Chain A: Q.45, E.48, H.127 Ligands: API.10 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.48, A:E.48, A:H.127, H2O.3 ZN.2: 2 residues within 4Å: Chain A: H.61, D.253 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.61, A:D.253, A:D.253, H2O.3, H2O.4 ZN.3: 2 residues within 4Å: Chain A: H.262, N.266 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.262, H2O.1, H2O.5, H2O.5 ZN.4: 2 residues within 4Å: Chain A: Q.319, E.320 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.320 ZN.5: 1 residues within 4Å: Chain A: D.99 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.99, A:D.99 ZN.6: 2 residues within 4Å: Chain A: E.187, H.189 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.187, A:H.189, H2O.5 ZN.7: 1 residues within 4Å: Chain A: H.373 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.373, H2O.2, H2O.2, H2O.3 ZN.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.9: 4 residues within 4Å: Chain A: N.381, V.382, F.385, E.395 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:V.382, A:F.385, A:E.395, A:E.395, H2O.4

1 x API: 2,6-DIAMINOPIMELIC ACID(Non-covalent)

API.10: 9 residues within 4Å: Chain A: N.92, R.93, H.125, H.127, W.147, M.202, T.207, E.221 Ligands: ZN.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.147 Hydrogen bonds: A:N.92, A:T.207, A:E.221 Water bridges: A:R.93, A:R.93 Salt bridges: A:R.93, A:H.125, A:H.127, A:H.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, H.S. et al., Structural basis for the recognition of muramyltripeptide by Helicobacter pylori Csd4, a D,L-carboxypeptidase controlling the helical cell shape. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-11-05

Peptides

Conserved hypothetical secreted protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Conserved hypothetical secreted protein

Related Entries With Identical Sequence