SMTL ID : 4wck.1

Crystal Structure of apo Cell Shape Determinant protein Csd4 from Helicobacter pylori

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

32 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: 2 residues within 4Å: Chain A: R.136, V.140 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: 5 residues within 4Å: Chain A: L.230, 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: 4 residues within 4Å: Chain A: N.85, F.324, K.326, L.331 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: 3 residues within 4Å: Chain A: R.34, H.39, L.70 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: 4 residues within 4Å: Chain A: K.301, I.302, P.303, K.318 Ligand excluded by PLIP IOD.17: 3 residues within 4Å: Chain A: Y.107, P.108, Q.111 Ligand excluded by PLIP IOD.18: 4 residues within 4Å: Chain A: Y.139, N.145, P.146, K.147 Ligand excluded by PLIP IOD.19: 5 residues within 4Å: Chain A: H.63, S.65, K.253, R.254, D.255 Ligand excluded by PLIP IOD.20: 5 residues within 4Å: Chain A: R.381, K.394, Y.425, N.427, N.428 Ligand excluded by PLIP IOD.21: 3 residues within 4Å: Chain A: A.142, M.143, R.148 Ligand excluded by PLIP IOD.22: 4 residues within 4Å: Chain A: Q.157, E.159, V.160, K.161 Ligand excluded by PLIP IOD.23: 3 residues within 4Å: Chain A: E.159, P.166, N.167 Ligand excluded by PLIP IOD.24: 5 residues within 4Å: Chain A: A.231, P.260, S.261, H.264 Ligands: IOD.27 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: N.259, P.260, S.261 Ligand excluded by PLIP IOD.27: 5 residues within 4Å: Chain A: P.229, A.231, S.232, P.260 Ligands: IOD.24 Ligand excluded by PLIP IOD.28: 4 residues within 4Å: Chain A: S.20, K.79, P.80, L.83 Ligand excluded by PLIP IOD.29: 3 residues within 4Å: Chain A: G.132, R.148, W.149 Ligand excluded by PLIP IOD.30: 4 residues within 4Å: Chain A: S.345, L.346, I.380, K.426 Ligand excluded by PLIP IOD.31: 3 residues within 4Å: Chain A: T.300, K.301, Q.304 Ligand excluded by PLIP IOD.32: 3 residues within 4Å: Chain A: K.301, P.303, Q.304 Ligand excluded by PLIP

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

API.33: 14 residues within 4Å: Chain A: N.94, R.95, H.127, H.129, W.149, I.154, D.156, M.204, A.207, L.208, T.209, F.210, A.221, E.223 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.149, A:A.221 Hydrogen bonds: A:N.94, A:L.208, A:T.209, A:T.209, A:E.223 Water bridges: A:Q.47, A:T.209, A:F.210 Salt bridges: A:R.95, A:H.127, A:H.129, A:H.129

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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