SMTL ID : 5fbc.1

S1 nuclease from Aspergillus oryzae in complex with 2'-deoxyadenosine-5'-thio-monophosphate (5'dAMP(S)).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

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

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

NAG.4: 4 residues within 4Å: Chain A: N.92, N.95, I.96, E.99 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.95, A:I.96 Hydrogen bonds: A:N.92 Water bridges: A:N.95 NAG.5: 7 residues within 4Å: Chain A: E.130, G.135, I.136, D.137, L.224, A.225, N.228 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.225 Hydrogen bonds: A:G.135, A:D.137, A:N.228

1 x AS: 2-DEOXY-ADENOSINE -5'-THIO-MONOPHOSPHATE(Non-covalent)

AS.6: 13 residues within 4Å: Chain A: K.48, Y.49, F.61, D.63, L.124, H.125, E.127, A.131, G.132, N.134, H.148, D.152 Ligands: ZN.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:N.134 Hydrogen bonds: A:K.48, A:Y.49, A:L.124 Water bridges: A:W.1, A:A.131 pi-Stacking: A:F.61, A:F.61

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 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:F.24, 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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