SMTL ID : 5yjj.2 (1 other biounit)

Crystal structure of PNPase from Staphylococcus epidermidis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-trimer

Ligands

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

PO4.1: 9 residues within 4Å: Chain A: R.415, H.419, S.450, G.452, S.453, S.454, S.455, K.510 Ligands: MG.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.450, A:S.453, A:S.454, A:S.454, A:S.455 Water bridges: A:G.452 Salt bridges: A:R.415, A:H.419, A:K.510 PO4.3: 10 residues within 4Å: Chain B: R.415, H.419, S.450, G.452, S.453, S.454, S.455, D.508, K.510 Ligands: MG.4 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.450, B:S.453, B:S.454, B:S.454, B:S.455, B:D.508 Water bridges: B:D.508, B:D.508 Salt bridges: B:R.415, B:H.419, B:K.510 PO4.5: 10 residues within 4Å: Chain C: R.415, H.419, S.450, G.452, S.453, S.454, S.455, D.508, K.510 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:S.450, C:S.453, C:S.453, C:S.454, C:S.454, C:S.455 Water bridges: C:D.508, C:K.510 Salt bridges: C:R.415, C:H.419, C:K.510

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: S.453, D.502, D.508 Ligands: PO4.1 No protein-ligand interaction detected (PLIP) MG.4: 6 residues within 4Å: Chain B: S.453, A.481, I.497, D.508, K.510 Ligands: PO4.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.508 MG.6: 6 residues within 4Å: Chain C: G.452, S.453, A.481, I.497, D.508 Ligands: PO4.5 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.508, H2O.22, H2O.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Raj, R. et al., Characterization of Staphylococcus epidermidis Polynucleotide phosphorylase and its interactions with ribonucleases RNase J1 and RNase J2. Biochem. Biophys. Res. Commun. (2018)

Release Date

2018-01-31

Peptides

Polyribonucleotide nucleotidyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Polyribonucleotide nucleotidyltransferase

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