SMTL ID : 5fba.1

S1 nuclease from Aspergillus oryzae in complex with phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

NAG.1: 7 residues within 4Å: Chain A: E.130, G.135, I.136, D.137, L.224, A.225, N.228 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.135, A:D.137, A:N.228

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain A: H.6, D.45, H.60, H.115, D.119 Ligands: ZN.4, PO4.5 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.1 ZN.3: 4 residues within 4Å: Chain A: H.125, H.148, D.152 Ligands: PO4.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.125, A:H.148, A:D.152, H2O.1, H2O.2 ZN.4: 7 residues within 4Å: Chain A: W.1, H.6, D.45, H.115, D.119 Ligands: ZN.2, PO4.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:W.1, A:H.6, A:D.119, H2O.1

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

PO4.5: 12 residues within 4Å: Chain A: W.1, H.6, D.45, K.48, H.60, H.115, D.119, H.125, D.152 Ligands: ZN.2, ZN.3, ZN.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.1, A:D.45 Water bridges: A:K.48 Salt bridges: A:K.48, A:H.60, A:H.115, A:H.125

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: F.24, N.27, I.28, P.101, N.102 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.27, A:I.28, A:N.102 Water bridges: A:N.27

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
A

Nuclease S1

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