SMTL ID : 2z1a.1

Crystal structure of 5'-nucleotidase precursor from Thermus thermophilus HB8

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 12 residues within 4Å: Chain A: H.39, D.83, N.115, H.116, H.238, H.240, R.345, R.349, R.383 Ligands: ZN.2, ZN.3, THM.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.115, A:N.115, A:H.238 Water bridges: A:H.215, A:R.349, A:R.349 Salt bridges: A:H.39, A:H.116, A:H.238, A:H.240, A:R.345, A:R.349, A:R.383

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: D.37, H.39, D.83, H.240 Ligands: PO4.1, ZN.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.37, A:H.39, A:D.83, H2O.2 ZN.3: 7 residues within 4Å: Chain A: D.37, D.83, N.115, H.215, H.238 Ligands: PO4.1, ZN.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.83, A:H.238, H2O.2

1 x THM: THYMIDINE(Non-covalent)

THM.4: 16 residues within 4Å: Chain A: N.115, H.116, D.119, I.179, N.181, N.378, G.380, G.381, R.383, F.402, N.404, G.432, R.433, F.481, D.487 Ligands: PO4.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.481, A:F.481 Hydrogen bonds: A:N.115, A:N.115, A:N.378, A:R.383, A:N.404, A:N.404 Water bridges: A:N.181, A:G.432, A:R.433, A:D.487 pi-Stacking: A:F.402, A:F.481

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakakaga, N. et al., Crystal structure of 5'-nucleotidase precursor from Thermus thermophilus HB8. To be Published

Release Date

2007-11-13

Peptides

5'-nucleotidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

5'-nucleotidase