SMTL ID : 8rza.1

Ribonuclease W

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x U- U- U: RNA (5'-R(P*UP*UP*U)-3')(Non-covalent)

U-U-U.1: 14 residues within 4Å: Chain A: R.10, H.92, P.152, V.157, I.159, K.170, I.171, S.172, R.173, K.174, L.199, R.201, T.202, R.242 Protein-ligand interaction information (PLIP) not available U-U-U.9: 14 residues within 4Å: Chain B: R.10, H.92, P.152, V.157, I.159, K.170, I.171, S.172, R.173, K.174, L.199, R.201, T.202, R.242 Protein-ligand interaction information (PLIP) not available

2 x U- A- U: RNA (5'-R(*UP*AP*U)-3')(Non-covalent)

U-A-U.2: 20 residues within 4Å: Chain A: H.326, K.328, I.334, I.336, R.355, K.361, F.362, Y.363, D.364, I.370, H.389, Y.391, F.402, N.404, D.420, E.422, D.424, D.437 Ligands: MG.7, MG.8 Protein-ligand interaction information (PLIP) not available U-A-U.10: 20 residues within 4Å: Chain B: H.326, K.328, I.334, I.336, R.355, K.361, F.362, Y.363, D.364, I.370, H.389, Y.391, F.402, N.404, D.420, E.422, D.424, D.437 Ligands: MG.15, MG.16 Protein-ligand interaction information (PLIP) not available

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

PO4.3: 6 residues within 4Å: Chain A: G.13, T.17, V.36, R.40, R.261, K.275 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.13, A:S.16, A:T.17, A:T.17 Salt bridges: A:R.40, A:R.261, A:K.275 PO4.6: 3 residues within 4Å: Chain A: R.12, D.35, K.45 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.35 Salt bridges: A:R.12, A:K.45 PO4.11: 6 residues within 4Å: Chain B: G.13, T.17, V.36, R.40, R.261, K.275 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.13, B:S.16, B:T.17 Salt bridges: B:R.40, B:R.261, B:K.275 PO4.14: 3 residues within 4Å: Chain B: R.12, D.35, K.45 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.35 Salt bridges: B:R.12, B:K.45

4 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 6 residues within 4Å: Chain A: I.80, W.385, A.457, R.460, I.461 Ligands: PG4.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.453, A:R.460, A:R.460 PG4.5: 6 residues within 4Å: Chain A: W.386, E.464, V.465, R.468, L.469 Ligands: PG4.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.468 Water bridges: A:R.427 PG4.12: 6 residues within 4Å: Chain B: I.80, W.385, A.457, R.460, I.461 Ligands: PG4.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.453, B:R.460, B:R.460 PG4.13: 6 residues within 4Å: Chain B: W.386, E.464, V.465, R.468, L.469 Ligands: PG4.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.468 Water bridges: B:R.427

4 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 5 residues within 4Å: Chain A: D.364, D.424, D.437 Ligands: U-A-U.2, U-A-U.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.364, A:D.437 MG.8: 5 residues within 4Å: Chain A: H.326, N.404, D.420, D.424 Ligands: U-A-U.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.420, A:D.424, H2O.1 MG.15: 5 residues within 4Å: Chain B: D.364, D.424, D.437 Ligands: U-A-U.10, U-A-U.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.364, B:D.437 MG.16: 5 residues within 4Å: Chain B: H.326, N.404, D.420, D.424 Ligands: U-A-U.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.420, B:D.424, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vayssieres, M. et al., RNase W, a conserved ribonuclease family with a novel active site. Nucleic Acids Res. (2024)

Release Date

2024-11-06

Peptides

Probable ribonuclease FAU-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Probable ribonuclease FAU-1