SMTL ID : 4q6o.1

Structural analysis of the mDAP-bound form of Helicobacter pylori Csd4, a D,L-carboxypeptidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

monomer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: Q.45, E.48, H.127 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.48, A:E.48, A:H.127, H2O.1, H2O.11 CA.2: 4 residues within 4Å: Chain A: N.381, V.382, F.385, E.395 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:V.382, A:F.385, A:E.395, H2O.3, H2O.6 CA.3: 2 residues within 4Å: Chain A: H.61, D.253 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.61, A:D.253, A:D.253, H2O.10

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

API.4: 11 residues within 4Å: Chain A: N.92, R.93, H.125, H.127, W.147, M.202, A.205, L.206, T.207, A.219, E.221 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.147, A:A.219 Hydrogen bonds: A:N.92, A:L.206, A:T.207, A:T.207, A:E.221 Water bridges: A:R.93, A:T.207, A:F.208 Salt bridges: A:R.93, A:H.125, A:H.127, A:H.127

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: I.305, S.307, A.309, Y.310, I.311, V.312 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.309, A:V.312 Water bridges: A:I.305, A:I.305, A:S.307 GOL.6: 4 residues within 4Å: Chain A: I.22, E.23, K.24, Y.310 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.23, A:K.24, A:K.24 Water bridges: A:E.23 GOL.7: 4 residues within 4Å: Chain A: N.297, T.298, K.316, Y.337 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.297 Water bridges: A:T.298 GOL.8: 2 residues within 4Å: Chain A: R.82, N.83 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.82, A:K.324 Water bridges: A:N.83, A:N.317, A:N.317, A:K.324

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

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