SMTL ID : 6a4f.1

Separated uridine bound Oligoribonuclease (ORN) from Colwellia psychrerythraea strain 34H

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

homo-dimer

Ligands

4 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U5P.1: 15 residues within 4Å: Chain A: D.14, L.15, E.16, M.17, T.18, G.19, L.20, N.61, W.63, C.64, H.68, H.160, D.165 Ligands: U5P.2, MN.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.16, A:M.17, A:G.19, A:G.19, A:N.61, A:H.68, A:D.165 Salt bridges: A:H.160 pi-Stacking: A:W.63, A:W.63 U5P.2: 9 residues within 4Å: Chain A: L.20, N.109, S.110, Q.113, S.137 Chain B: Y.131, R.132 Ligands: U5P.1, MN.3 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:Y.131, A:N.109, A:S.110, A:S.137 Salt bridges: B:R.132, A:K.140 pi-Stacking: B:Y.131 Water bridges: A:Q.113 U5P.4: 15 residues within 4Å: Chain B: D.14, L.15, E.16, M.17, T.18, G.19, L.20, N.61, W.63, C.64, H.68, H.160, D.165 Ligands: U5P.5, MN.6 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:E.16, B:M.17, B:G.19, B:N.61, B:H.68, B:D.165 Water bridges: B:L.15 Salt bridges: B:H.160 pi-Stacking: B:W.63, B:W.63 U5P.5: 9 residues within 4Å: Chain A: Y.131, R.132 Chain B: L.20, N.109, S.110, Q.113, S.137 Ligands: U5P.4, MN.6 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:Y.131, B:N.109, B:S.110, B:S.137, B:S.137 Salt bridges: A:R.132, B:K.140 pi-Stacking: A:Y.131 Water bridges: B:D.114

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 4 residues within 4Å: Chain A: D.14, L.15 Ligands: U5P.1, U5P.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.14, U5P.1 MN.6: 4 residues within 4Å: Chain B: D.14, L.15 Ligands: U5P.4, U5P.5 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.14, H2O.5, H2O.5, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, C.W. et al., Structural basis of small RNA hydrolysis by oligoribonuclease (CpsORN) from Colwellia psychrerythraea strain 34H. Sci Rep (2019)

Release Date

2019-03-13

Peptides

Oligoribonuclease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Oligoribonuclease