SMTL ID : 5cyr.1

Crystal structure of Thosea asigna virus RNA-dependent RNA polymerase (RdRP) complexed with ATP and ssRNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-dimer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 13 residues within 4Å: Chain A: R.195, K.309, R.311, D.382, D.383, F.401, K.402, Q.403, K.519, L.544, G.545, Y.642, F.644 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.382, A:D.382, A:Q.403, A:Q.403 Salt bridges: A:R.195, A:K.309, A:K.309, A:R.311, A:R.311, A:K.519, A:K.519

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

SO4.2: 4 residues within 4Å: Chain A: V.471, G.473, T.474, T.475 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.473, A:T.475, A:T.475 SO4.5: 5 residues within 4Å: Chain B: V.471, V.472, G.473, T.474, T.475 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.473, B:T.474, B:T.475

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

PO4.3: 4 residues within 4Å: Chain A: A.245, S.246, K.295, Y.313 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.246, A:Y.313 Salt bridges: A:K.295 PO4.6: 3 residues within 4Å: Chain A: R.43 Chain B: T.241, N.242 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.43 Hydrogen bonds: B:N.242 PO4.7: 4 residues within 4Å: Chain B: A.245, S.246, K.295, Y.313 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.246, B:S.246 Salt bridges: B:K.295 PO4.8: 4 residues within 4Å: Chain A: T.241, N.242, K.255 Chain B: R.43 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.241, A:T.241, A:N.242 Salt bridges: A:K.255, B:R.43

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 2 residues within 4Å: Chain B: R.66, K.67 No protein-ligand interaction detected (PLIP)

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

2015-11-11

Peptides

RNA-dependent RNA polymerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

RNA-dependent RNA polymerase

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