SMTL ID : 7qta.2 (1 other biounit)

S1 nuclease from Aspergillus oryzae in complex with uridine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.06 Å

Oligo State

monomer

Ligands

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

BTB.1: 3 residues within 4Å: Chain A: T.153, 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:H.149, A:E.157, A:E.157, A:E.157 Salt bridges: A:E.157 BTB.9: 3 residues within 4Å: Chain A: D.199, V.201, S.202 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.199, A:S.202 Water bridges: A:D.199, A:V.201 Salt bridges: A:D.199

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain A: W.1, H.6, D.45, H.115, D.119 Ligands: ZN.3, PO4.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:W.1, A:H.6, A:D.119, H2O.8 ZN.3: 6 residues within 4Å: Chain A: D.45, H.60, H.115, D.119 Ligands: ZN.2, PO4.7 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.8 ZN.4: 5 residues within 4Å: Chain A: H.125, H.148, D.152 Ligands: PO4.7, URI.8 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.10

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

NAG.5: 4 residues within 4Å: Chain A: F.55, Y.59, N.92, Y.93 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.59, 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 PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 14 residues within 4Å: Chain A: W.1, H.6, D.45, K.48, H.60, H.115, D.119, H.125, H.148, D.152 Ligands: ZN.2, ZN.3, ZN.4, URI.8 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:W.1, A:D.45 Water bridges: A:D.45, A:K.48, A:D.152, A:D.152 Salt bridges: A:K.48, A:H.60, A:H.115, A:H.125

1 x URI: URIDINE(Non-covalent)

URI.8: 12 residues within 4Å: Chain A: K.48, H.60, F.61, D.63, L.124, H.125, A.131, G.132, N.134, H.148 Ligands: ZN.4, PO4.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.63, A:N.134 Water bridges: A:K.48, A:K.48, A:D.152 pi-Stacking: A:F.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adamkova, K. et al., Atomic resolution studies of S1 nuclease complexes reveal details of RNA interaction with the enzyme despite multiple lattice-translocation defects. Acta Crystallogr D Struct Biol (2022)

Release Date

2022-11-09

Peptides

Nuclease S1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Nuclease S1

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