SMTL ID : 4xha.1

Crystal structure of Thosea asigna virus RNA-dependent RNA polymerase (RdRP) complexed with Lu3+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

2 x LU: LUTETIUM (III) ION(Non-covalent)

LU.1: 1 residues within 4Å: Chain A: D.171 No protein-ligand interaction detected (PLIP) LU.8: 2 residues within 4Å: Chain B: D.171, D.173 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.173

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: R.300, P.575, R.576, R.595, A.641 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.576 Salt bridges: A:R.300, A:R.576, A:R.595 SO4.3: 7 residues within 4Å: Chain A: S.328, V.471, V.472, G.473, T.474, T.475 Chain B: P.41 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.328, A:S.328, A:G.473, A:T.474, A:T.475, A:T.475 SO4.4: 4 residues within 4Å: Chain A: A.245, S.246, K.295, Y.313 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.246 Salt bridges: A:K.295 SO4.7: 7 residues within 4Å: Chain A: R.195, K.309, R.311, F.401, K.402, Q.403, K.519 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.403 Salt bridges: A:R.195, A:K.309, A:K.519 SO4.9: 5 residues within 4Å: Chain B: R.300, P.575, R.576, R.595, A.641 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.576 Salt bridges: B:R.300, B:R.576, B:R.595 SO4.10: 5 residues within 4Å: Chain B: S.328, V.471, G.473, T.474, T.475 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.328, B:G.473, B:T.474, B:T.475, B:T.475, B:T.475 SO4.11: 4 residues within 4Å: Chain B: A.245, S.246, K.295, Y.313 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.246, B:Y.313, B:S.315, B:S.315 Salt bridges: B:K.295 SO4.12: 6 residues within 4Å: Chain B: R.195, K.309, R.311, F.401, K.402, Q.403 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.403 Salt bridges: B:R.195, B:K.309, B:R.311

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: P.77, R.611, Y.659, S.661, Y.662, D.663 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.659, A:Y.659, A:Y.662, A:D.663 GOL.6: 5 residues within 4Å: Chain A: T.140, H.141, S.148, V.149, K.150 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferrero, D.S. et al., The Structure of the RNA-Dependent RNA Polymerase of a Permutotetravirus Suggests a Link between Primer-Dependent and Primer-Independent Polymerases. Plos Pathog. (2015)

Release Date

2015-11-04

Peptides

RNA-dependent RNA polymerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

RNA-dependent RNA polymerase

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