SMTL ID : 9ftw.1 (1 other biounit)

Crystal structure of calcium-activated EndoU

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 5 residues within 4Å: Chain A: L.163, D.326, S.327, Y.328, D.330 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.328, A:D.330 Hydrogen bonds: A:D.326 Water bridges: A:Y.328, A:Y.328, A:Y.328

5 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: Y.209, Q.210, E.217, D.279, S.280, E.284 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Q.210, A:E.217, A:D.279, H2O.1, H2O.2 CA.3: 6 residues within 4Å: Chain A: N.204, L.205, N.207, N.208, E.223, E.226 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.204, A:E.226, A:E.226, H2O.7, H2O.8 CA.4: 6 residues within 4Å: Chain A: D.179, C.181, P.182, D.315, Y.316, Y.317 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.181, A:D.315, A:Y.316, H2O.4, H2O.7 CA.5: 6 residues within 4Å: Chain A: D.134, A.135, I.136, T.137, E.140, Q.250 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.135, A:E.140, A:E.140, H2O.5 CA.6: 5 residues within 4Å: Chain A: D.322, G.323, W.325, D.326, D.330 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.322, A:G.323, A:W.325, A:D.330, H2O.6

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 8 residues within 4Å: Chain A: H.285, T.297, G.298, H.300, K.343, V.345, T.403, Y.405 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.285, A:K.343, A:T.403 Water bridges: A:G.298, A:G.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malard, F. et al., Molecular Basis for the Calcium-Dependent Activation of the Ribonuclease EndoU. Res Sq (2024)

Release Date

2024-08-14

Peptides

Uridylate-specific endoribonuclease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Uridylate-specific endoribonuclease

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