SMTL ID : 5fb9.2 (1 other biounit)

S1 nuclease from Aspergillus oryzae with unoccupied active site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.1: 2 residues within 4Å: Chain A: E.157, Y.163 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.157 Water bridges: A:N.3, A:N.3, A:N.3, A:H.149, A:T.153, A:E.157 Salt bridges: A:E.157

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: W.1, H.6, D.45, H.115, D.119 Ligands: ZN.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:W.1, A:H.6, A:D.119, H2O.3 ZN.3: 6 residues within 4Å: Chain A: H.6, D.45, H.60, H.115, D.119 Ligands: ZN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.45, A:H.60, A:H.115, A:D.119, H2O.3 ZN.4: 3 residues within 4Å: Chain A: H.125, H.148, D.152 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.125, A:H.148, A:D.152, H2O.5, H2O.11

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.5: 6 residues within 4Å: Chain A: F.55, Y.59, N.92, Y.93, I.96, E.105 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Y.59, A:N.92, A:N.92, A:N.92 NAG.6: 5 residues within 4Å: Chain A: E.130, G.135, L.224, A.225, N.228 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.225 Hydrogen bonds: A:N.228 Water bridges: A:E.130, A:G.135, A:G.135, A:D.137

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

NA.7: 1 residues within 4Å: Chain A: N.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koval, T. et al., Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition. PLoS ONE (2016)

Release Date

2016-12-28

Peptides

Nuclease S1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Nuclease S1

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