SMTL ID : 4y4v.1

Structure of Helicobacter pylori Csd6 in the D-Ala-bound state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-dimer

Ligands

3 x DAL: D-ALANINE(Non-covalent)

DAL.1: 6 residues within 4Å: Chain A: K.116, E.119, G.120, G.163, H.164 Ligands: DAL.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.119, A:G.120, A:D.121, A:H.164, A:H.164 Water bridges: A:L.122, A:A.123 Salt bridges: A:K.116 DAL.2: 5 residues within 4Å: Chain A: Y.142, G.165, W.167, C.185 Ligands: DAL.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.142, A:W.167 Hydrogen bonds: A:G.165 DAL.5: 7 residues within 4Å: Chain B: K.116, E.119, G.120, G.163, H.164, I.166, K.183 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.166 Hydrogen bonds: B:G.120, B:D.121, B:H.164, B:H.164, B:H.164 Salt bridges: B:K.116, B:H.164

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: F.70, V.81, E.90, Y.92, Y.210 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.210 Water bridges: A:N.83, A:F.214 GOL.4: 6 residues within 4Å: Chain A: A.280, K.307 Chain B: Q.38, K.39, Q.40, G.41 No protein-ligand interaction detected (PLIP) GOL.6: 7 residues within 4Å: Chain B: W.236, Y.266, K.267, V.270, F.271, K.277, Y.306 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.266, B:Y.266, B:K.267, B:K.277, B:K.277, B:Y.306 GOL.7: 3 residues within 4Å: Chain B: V.81, E.90, Y.210 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.90 Water bridges: B:V.81, B:E.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, H.S. et al., The Cell Shape-determining Csd6 Protein from Helicobacter pylori Constitutes a New Family of l,d-Carboxypeptidase. J.Biol.Chem. (2015)

Release Date

2015-09-02

Peptides

Conserved hypothetical secreted protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Conserved hypothetical secreted protein

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