SMTL ID : 3exm.1

Crystal structure of the phosphatase SC4828 with the non-hydrolyzable nucleotide GPCP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: Y.132, N.134, D.150, D.154 Ligands: CA.2, GP2.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.150, A:D.150, A:D.154, H2O.1 CA.2: 6 residues within 4Å: Chain A: F.152, D.154, D.167 Ligands: CA.1, CA.3, GP2.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.152, A:D.154, A:D.167, H2O.4, H2O.13 CA.3: 3 residues within 4Å: Chain A: D.167 Ligands: CA.2, GP2.6 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.167, H2O.7, H2O.9, H2O.13, H2O.13

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

NA.4: 0 residues within 4Å: (No contacts) 3 PLIP interactions: 3 interactions with chain A Water bridges: A:A.57, A:A.57, A:P.112 NA.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x GP2: PHOSPHOMETHYLPHOSPHONIC ACID GUANOSYL ESTER(Non-covalent)

GP2.6: 14 residues within 4Å: Chain A: W.101, F.102, T.104, F.121, Y.132, N.134, D.150, F.152, D.154, R.166, D.167 Ligands: CA.1, CA.2, CA.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:F.102, A:F.102, A:F.102, A:Y.132, A:Y.132, A:D.150, A:R.166 Water bridges: A:R.48, A:R.48, A:T.104, A:T.104, A:E.170 pi-Stacking: A:W.101, A:F.102 pi-Cation interactions: A:F.102

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: L.153, W.165, E.168, F.171, R.189 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.165, A:R.189 Water bridges: A:R.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Proudfoot, M. et al., Structure and mechanism of a new family of prokaryotic nucleoside diphosphatases. To be Published

Release Date

2008-12-09

Peptides

Phosphatase SC4828: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphatase SC4828

Related Entries With Identical Sequence