SMTL ID : 4xhi.1

Crystal structure of native Thosea asigna virus RNA-dependent RNA polymerase (RdRP) at 2.15 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: R.93, S.97 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.97, A:S.97 Salt bridges: A:R.93 SO4.2: 5 residues within 4Å: Chain A: R.300, P.575, R.576, R.595, A.641 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.576 Water bridges: A:R.300, A:R.300 Salt bridges: A:R.300, A:R.576, A:R.595 SO4.3: 6 residues within 4Å: Chain A: R.195, K.309, R.311, F.401, Q.403 Ligands: GOL.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.403 Salt bridges: A:R.195, A:K.309, A:R.311 SO4.4: 1 residues within 4Å: Chain A: K.372 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.372, A:K.372 Salt bridges: A:K.372 SO4.5: 5 residues within 4Å: Chain A: P.77, R.611, Y.659, S.661, Y.662 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.659, A:Y.662 Water bridges: A:R.611, A:R.611, A:R.611, A:D.663 Salt bridges: A:R.611 SO4.6: 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 Water bridges: A:K.295 Salt bridges: A:K.295 SO4.13: 5 residues within 4Å: Chain A: V.471, V.472, G.473, T.474, T.475 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.473, A:T.474, A:T.475, A:T.475 Water bridges: A:Y.348, A:Y.348 SO4.14: 5 residues within 4Å: Chain B: R.300, P.575, R.576, R.595, A.641 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.576 Water bridges: B:R.300, B:R.300 Salt bridges: B:R.300, B:R.576, B:R.595 SO4.15: 1 residues within 4Å: Chain B: K.464 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.464 SO4.16: 2 residues within 4Å: Chain B: R.85, R.168 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.85, B:R.168 SO4.22: 5 residues within 4Å: Chain B: V.471, V.472, G.473, T.474, T.475 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.473, B:T.474, B:T.475, B:T.475, B:T.475 Water bridges: B:L.476 SO4.23: 6 residues within 4Å: Chain B: R.195, K.309, R.311, F.401, K.402, Q.403 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.403 Water bridges: B:R.195, B:R.195, B:D.382, B:M.404 Salt bridges: B:R.195, B:K.309, B:R.311 SO4.24: 4 residues within 4Å: Chain B: A.245, S.246, K.295, Y.313 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.246, B:Y.313, B:Y.313 Salt bridges: B:K.295

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: R.53, R.66, K.67, S.690 Chain B: H.133 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.53, A:R.66, A:K.67, A:S.690, A:S.690 GOL.8: 7 residues within 4Å: Chain A: P.124, V.125, C.126, G.127, K.285, H.286, P.287 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.124, A:G.127, A:K.285, A:H.286 GOL.9: 6 residues within 4Å: Chain A: Y.380, G.381, D.382, D.383, L.544, F.644 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.382, A:D.382, A:D.383 GOL.10: 3 residues within 4Å: Chain A: T.140, H.141, K.150 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.141, A:K.150 Water bridges: A:N.142, A:S.148, A:V.149 GOL.11: 3 residues within 4Å: Chain A: T.254, R.256, D.257 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.256 GOL.12: 4 residues within 4Å: Chain A: K.309, K.402, K.519 Ligands: SO4.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.309 GOL.17: 2 residues within 4Å: Chain B: R.283, R.460 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.460, B:R.460 GOL.18: 5 residues within 4Å: Chain B: Y.380, G.381, D.382, L.544, F.644 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.382 Water bridges: B:D.478 GOL.19: 5 residues within 4Å: Chain B: K.277, D.278, L.279, T.280, R.283 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.279, B:T.280, B:T.280, B:R.283 GOL.20: 3 residues within 4Å: Chain B: T.254, R.256, D.257 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.254, B:T.254, B:R.256 Water bridges: B:D.257 GOL.21: 4 residues within 4Å: Chain B: G.139, T.140, H.141, K.150 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.141 Water bridges: B:K.150, B: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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