SMTL ID : 7vh4.1 (1 other biounit)

Crystal structure of oligoribonuclease of Escherichia coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

ACT.1: 4 residues within 4Å: Chain A: N.108, S.109 Chain B: Y.130, R.131 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:N.108 Hydrogen bonds: A:S.109, B:Y.130 Water bridges: A:N.108, A:K.139 Salt bridges: B:R.131 ACT.4: 5 residues within 4Å: Chain A: Y.130, R.131 Chain B: N.108, S.109, S.136 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.131 Hydrogen bonds: B:N.108, B:S.109

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 3 residues within 4Å: Chain A: K.139, R.143 Chain B: R.131 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.131, B:R.131, A:K.139

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.13, L.14, E.15 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.13, A:E.15, H2O.1, H2O.2 MG.5: 1 residues within 4Å: Chain B: D.13 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.13, H2O.2, H2O.3, H2O.3, H2O.3

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

NA.6: 4 residues within 4Å: Chain B: R.114, E.125, A.126, F.128 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.114, B:E.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Badhwar, P. et al., Three-dimensional structure of a mycobacterial oligoribonuclease reveals a unique C-terminal tail that stabilizes the homodimer. J.Biol.Chem. (2022)

Release Date

2022-09-28

Peptides

Oligoribonuclease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Oligoribonuclease

Related Entries With Identical Sequence