SMTL ID : 4rny.1 (2 other biounits)

Structure of Helicobacter pylori Csd3 from the orthorhombic crystal

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: E.34, H.219, D.223, H.301 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.34, A:H.219, A:D.223, A:D.223, A:H.301

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: Q.64, D.65, F.86, R.88, D.144, R.309 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.64, A:D.144 Water bridges: A:T.155 Salt bridges: A:R.88, A:R.309 SO4.3: 5 residues within 4Å: Chain A: Q.167, Y.168, Y.169, D.180, S.181 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.167, A:Y.169, A:S.181 SO4.4: 5 residues within 4Å: Chain A: N.42, V.43, T.44, F.151, G.152 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.42, A:T.44, A:G.152 Water bridges: A:T.44 SO4.5: 2 residues within 4Å: Chain A: H.350, L.360 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.350

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: S.205, Y.206, R.216 Ligands: GOL.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.206, A:R.216, A:R.216 GOL.7: 5 residues within 4Å: Chain A: T.10, L.11, L.12, K.246, A.247 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.10, A:L.11, A:L.12, A:A.247 GOL.8: 7 residues within 4Å: Chain A: S.63, Q.64, D.65, Y.206, R.309, P.310, I.311 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.63, A:Q.64, A:Y.206, A:R.309 Water bridges: A:D.65 GOL.9: 4 residues within 4Å: Chain A: N.175, F.204, N.312 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.175, A:N.312

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

An, D.R. et al., Structure of Csd3 from Helicobacter pylori, a cell shape-determining metallopeptidase. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-03-11

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