SMTL ID : 5fbf.1

S1 nuclease from Aspergillus oryzae in complex with two molecules of 2'-deoxycytidine-5'-monophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.04 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: W.1, H.6, D.45, D.119 Ligands: ZN.2, DCM.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:W.1, A:H.6, A:D.119, DCM.7 ZN.2: 7 residues within 4Å: Chain A: D.45, K.48, H.60, H.115, D.119 Ligands: ZN.1, DCM.7 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.45, A:H.60, A:H.115, A:D.119, DCM.7 ZN.3: 5 residues within 4Å: Chain A: H.125, H.148, D.152 Ligands: DCM.6, DCM.7 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.125, A:H.148, A:D.152, A:D.152, DCM.7

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

NAG.4: 6 residues within 4Å: Chain A: F.55, Y.59, N.92, Y.93, I.96, E.105 5 PLIP interactions: 5 interactions with chain A Water bridges: A:Y.59, A:N.92, A:Y.93, A:E.105, A:E.105 NAG.5: 5 residues within 4Å: Chain A: G.135, I.136, 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

2 x DCM: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

DCM.6: 11 residues within 4Å: Chain A: K.48, Y.49, F.61, D.63, H.125, A.131, G.132, N.134, H.148 Ligands: ZN.3, DCM.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.48, A:K.48, A:Y.49, A:D.63, A:N.134 pi-Stacking: A:F.61 DCM.7: 16 residues within 4Å: Chain A: W.1, G.2, H.6, D.45, K.48, Y.49, H.60, H.115, D.119, H.125, H.148, D.152 Ligands: ZN.1, ZN.2, ZN.3, DCM.6 5 PLIP interactions: 5 interactions with chain A Water bridges: A:N.3, A:N.3, A:T.153 Salt bridges: A:K.48, A:H.125

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

NA.8: 3 residues within 4Å: Chain A: S.186, D.189, S.190 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.189

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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