SMTL ID : 4wcn.1

Crystal Structure of Tripeptide bound Cell Shape Determinant Csd4 protein from Helicobacter pylori

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

41 x IOD: IODIDE ION(Non-functional Binders)

IOD.1: 4 residues within 4Å: Chain A: P.51, L.230, N.329, K.330 Ligand excluded by PLIP IOD.2: 4 residues within 4Å: Chain A: R.136, V.140, L.144 Ligands: NA.44 Ligand excluded by PLIP IOD.3: 4 residues within 4Å: Chain A: F.165, P.166, N.167, F.171 Ligand excluded by PLIP IOD.4: 6 residues within 4Å: Chain A: L.230, A.231, H.264, I.267, N.268, K.330 Ligand excluded by PLIP IOD.5: 5 residues within 4Å: Chain A: R.84, I.302, P.303, V.317, K.318 Ligand excluded by PLIP IOD.6: 3 residues within 4Å: Chain A: N.85, F.324, K.326 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: R.136, P.137, V.138 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: R.84, N.319 Ligand excluded by PLIP IOD.9: 4 residues within 4Å: Chain A: R.34, H.39, L.70, N.121 Ligand excluded by PLIP IOD.10: 3 residues within 4Å: Chain A: A.37, P.38, K.164 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: A.170, N.174 Ligand excluded by PLIP IOD.12: 4 residues within 4Å: Chain A: P.297, H.298, E.341, F.342 Ligand excluded by PLIP IOD.13: 4 residues within 4Å: Chain A: K.350, D.357, Q.358, M.359 Ligand excluded by PLIP IOD.14: 5 residues within 4Å: Chain A: N.292, H.293, I.385, F.411, R.421 Ligand excluded by PLIP IOD.15: 4 residues within 4Å: Chain A: Q.157, R.196, A.198, Q.199 Ligand excluded by PLIP IOD.16: 3 residues within 4Å: Chain A: Y.107, P.108, Q.111 Ligand excluded by PLIP IOD.17: 4 residues within 4Å: Chain A: Y.139, N.145, P.146, K.147 Ligand excluded by PLIP IOD.18: 6 residues within 4Å: Chain A: H.63, Y.64, S.65, K.253, R.254, D.255 Ligand excluded by PLIP IOD.19: 3 residues within 4Å: Chain A: Q.408, K.409, R.410 Ligand excluded by PLIP IOD.20: 3 residues within 4Å: Chain A: A.142, M.143, R.148 Ligand excluded by PLIP IOD.21: 3 residues within 4Å: Chain A: K.119, P.120, N.121 Ligand excluded by PLIP IOD.22: 2 residues within 4Å: Chain A: N.249, P.251 Ligand excluded by PLIP IOD.23: 3 residues within 4Å: Chain A: E.159, P.166, N.167 Ligand excluded by PLIP IOD.24: 4 residues within 4Å: Chain A: P.260, S.261, H.264 Ligands: IOD.28 Ligand excluded by PLIP IOD.25: 2 residues within 4Å: Chain A: K.253, R.254 Ligand excluded by PLIP IOD.26: 3 residues within 4Å: Chain A: R.254, E.257, L.258 Ligand excluded by PLIP IOD.27: 3 residues within 4Å: Chain A: N.259, P.260, S.261 Ligand excluded by PLIP IOD.28: 5 residues within 4Å: Chain A: P.229, A.231, S.232, P.260 Ligands: IOD.24 Ligand excluded by PLIP IOD.29: 4 residues within 4Å: Chain A: S.20, K.79, P.80, L.83 Ligand excluded by PLIP IOD.30: 4 residues within 4Å: Chain A: G.132, R.148, W.149 Ligands: 3KS.45 Ligand excluded by PLIP IOD.31: 4 residues within 4Å: Chain A: H.264, A.265, N.268, K.270 Ligand excluded by PLIP IOD.32: 4 residues within 4Å: Chain A: S.345, L.346, I.380, K.426 Ligand excluded by PLIP IOD.33: 3 residues within 4Å: Chain A: T.300, K.301, Q.304 Ligand excluded by PLIP IOD.34: 4 residues within 4Å: Chain A: K.301, P.303, Q.304 Ligands: NA.43 Ligand excluded by PLIP IOD.35: 6 residues within 4Å: Chain A: Q.352, N.355, S.371, F.372, Y.373, T.401 Ligand excluded by PLIP IOD.36: 3 residues within 4Å: Chain A: R.403, F.404, K.405 Ligand excluded by PLIP IOD.37: 3 residues within 4Å: Chain A: W.273, K.275, E.308 Ligand excluded by PLIP IOD.38: 2 residues within 4Å: Chain A: R.381, N.396 Ligand excluded by PLIP IOD.39: 2 residues within 4Å: Chain A: L.184, P.260 Ligand excluded by PLIP IOD.40: 4 residues within 4Å: Chain A: K.26, A.27, S.65, V.66 Ligand excluded by PLIP IOD.41: 4 residues within 4Å: Chain A: S.277, P.297, I.305, P.306 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.42: 5 residues within 4Å: Chain A: Q.47, E.50, R.87, H.129 Ligands: 3KS.45 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.50, A:E.50, A:H.129, H2O.4

2 x NA: SODIUM ION(Non-functional Binders)

NA.43: 3 residues within 4Å: Chain A: K.301, P.303 Ligands: IOD.34 No protein-ligand interaction detected (PLIP) NA.44: 3 residues within 4Å: Chain A: R.136, I.187 Ligands: IOD.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.136, A:R.136, A:P.186

1 x 3KS: N-acetyl-L-alanyl-N-[(1S,5R)-5-amino-1,5-dicarboxypentyl]-D-glutamine(Non-covalent)

3KS.45: 20 residues within 4Å: Chain A: Q.47, R.87, D.92, N.94, R.95, H.127, H.129, G.131, G.132, W.149, I.154, M.204, A.207, L.208, T.209, A.221, E.223, K.226 Ligands: IOD.30, ZN.42 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:W.149, A:W.149, A:A.221 Hydrogen bonds: A:R.87, A:N.94, A:G.132, A:W.149, A:L.208, A:T.209 Water bridges: A:R.87, A:R.95, A:R.95, A:D.156, A:D.156, A:T.209, A:F.210, A:K.226 Salt bridges: A:R.95, A:H.127, A:H.129, A:K.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chan, A.C. et al., Helical Shape of Helicobacter pylori Requires an Atypical Glutamine as a Zinc Ligand in the Carboxypeptidase Csd4. J.Biol.Chem. (2015)

Release Date

2014-12-24

Peptides

Conserved hypothetical secreted protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Conserved hypothetical secreted protein

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