SMTL ID : 5xex.1 (1 other biounit)

Crystal structure of S.aureus PNPase catalytic domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-trimer

Ligands

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

PEG.1: 7 residues within 4Å: Chain A: K.306, R.310, A.491, G.493, D.494, K.514, I.515 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.306, A:R.310, A:A.491, A:D.494 PEG.4: 7 residues within 4Å: Chain B: K.306, R.310, A.491, G.493, D.494, K.514, I.515 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.306, B:A.491, B:D.494 PEG.7: 7 residues within 4Å: Chain C: K.306, R.310, A.491, G.493, D.494, K.514, I.515 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.306, C:A.491, C:D.494

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: L.102, Q.146, H.182, D.516 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.182 GOL.5: 4 residues within 4Å: Chain B: L.102, Q.146, H.182, D.516 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.182 GOL.8: 4 residues within 4Å: Chain C: L.102, Q.146, H.182, D.516 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.182

3 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.3: 9 residues within 4Å: Chain A: R.403, H.407, G.440, S.441, S.442, S.443, D.490, D.496, K.498 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.440, A:S.442, A:S.443 Salt bridges: A:R.403, A:R.403, A:H.407, A:H.407, A:K.498, A:K.498 PPV.6: 9 residues within 4Å: Chain B: R.403, H.407, G.440, S.441, S.442, S.443, D.490, D.496, K.498 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.440, B:S.442, B:S.443 Salt bridges: B:R.403, B:R.403, B:H.407, B:H.407, B:K.498, B:K.498 PPV.9: 9 residues within 4Å: Chain C: R.403, H.407, G.440, S.441, S.442, S.443, D.490, D.496, K.498 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:G.440, C:S.442, C:S.443 Salt bridges: C:R.403, C:R.403, C:H.407, C:H.407, C:K.498, C:K.498

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, X. et al., Enolase binds to RnpA in competition with PNPase in Staphylococcus aureus. FEBS Lett. (2017)

Release Date

2017-10-18

Peptides

Polyribonucleotide nucleotidyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Polyribonucleotide nucleotidyltransferase

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