SMTL ID : 5fbb.1 (1 other biounit)

S1 nuclease from Aspergillus oryzae in complex with phosphate and adenosine 5'-monophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

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

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

NAG.4: 5 residues within 4Å: Chain A: Y.59, N.92, Y.93, I.96, E.105 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.92 NAG.5: 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

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

PO4.6: 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.1, ZN.2, ZN.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.1 Water bridges: A:W.1, A:K.48 Salt bridges: A:K.48, A:H.60, A:H.115, A:H.125

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.7: 11 residues within 4Å: Chain A: K.57, F.61, D.63, L.124, H.125, E.127, A.131, G.132, N.134, H.148 Ligands: NA.8 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.57, A:D.63, A:N.134 Water bridges: A:D.63, A:D.63, A:D.63, A:A.131, A:A.131 pi-Stacking: A:F.61, A:F.61, A:H.125

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

NA.8: 2 residues within 4Å: Chain A: D.63 Ligands: AMP.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.63, A:D.63 NA.9: 2 residues within 4Å: Chain A: L.98 Ligands: ETE.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.98

3 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.10: 3 residues within 4Å: Chain A: D.189, D.193 Ligands: BTB.13 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.189, A:D.193, H2O.3 CA.11: 1 residues within 4Å: Ligands: BTB.14 No protein-ligand interaction detected (PLIP) CA.12: 1 residues within 4Å: Chain A: S.186 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.186, H2O.6

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

BTB.13: 4 residues within 4Å: Chain A: D.189, T.192, D.193 Ligands: CA.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.192, A:D.193 Water bridges: A:D.193, A:G.194 BTB.14: 5 residues within 4Å: Chain A: N.3, T.153, E.157, Y.163 Ligands: CA.11 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.3, A:E.157, A:Y.163 Water bridges: A:N.3, A:L.4, A:L.4, A:Y.163 Salt bridges: A:E.157

1 x ETE: 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-covalent)

ETE.15: 6 residues within 4Å: Chain A: L.98, E.99, P.101, A.263, S.264 Ligands: NA.9 No protein-ligand interaction detected (PLIP)

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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