SMTL ID : 5cx6.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

12 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.595 Salt bridges: A:R.300, A:R.576, A:R.595 SO4.3: 4 residues within 4Å: Chain A: K.277, D.278, L.279, T.280 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.279, A:T.280, A:T.280 Water bridges: A:K.277 Salt bridges: A:K.277 SO4.4: 6 residues within 4Å: Chain A: V.471, V.472, G.473, T.474, T.475 Chain B: P.41 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:P.41, A:G.473, A:T.474, A:T.475, A:T.475 Water bridges: A:S.328, A:Y.348 SO4.5: 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 SO4.6: 2 residues within 4Å: Chain A: R.85, R.168 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.168 SO4.7: 7 residues within 4Å: Chain A: R.195, K.309, R.311, F.401, K.402, Q.403, K.519 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Q.403 Water bridges: A:R.195, A:R.195, A:R.195, A:R.195, A:Q.403, A:M.404 Salt bridges: A:R.195, A:K.309, A:R.311, A:K.519 SO4.22: 5 residues within 4Å: Chain B: P.77, R.611, Y.659, S.661, Y.662 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.611, B:Y.659, B:Y.662 SO4.23: 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 SO4.24: 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:Y.313 Salt bridges: B:K.295 SO4.25: 6 residues within 4Å: Chain B: S.328, V.471, V.472, 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 Water bridges: B:L.476 SO4.26: 7 residues within 4Å: Chain B: R.195, K.309, R.311, F.401, K.402, Q.403, K.519 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Q.403 Water bridges: B:R.195, B:K.309, B:D.382, B:D.382, B:K.519 Salt bridges: B:R.195, B:K.309, B:R.311, B:K.519

19 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 6 residues within 4Å: Chain A: Y.380, G.381, D.382, D.478, F.644 Ligands: GOL.12 Ligand excluded by PLIP GOL.9: 1 residues within 4Å: Chain A: K.464 Ligand excluded by PLIP GOL.10: 2 residues within 4Å: Chain A: Y.123 Ligands: GOL.11 Ligand excluded by PLIP GOL.11: 2 residues within 4Å: Chain A: R.460 Ligands: GOL.10 Ligand excluded by PLIP GOL.12: 6 residues within 4Å: Chain A: L.544, A.641, Y.642, A.643, F.644 Ligands: GOL.8 Ligand excluded by PLIP GOL.13: 7 residues within 4Å: Chain A: H.141, V.149, K.150, R.151, E.293, K.295 Ligands: GOL.16 Ligand excluded by PLIP GOL.14: 4 residues within 4Å: Chain A: R.53, R.66, K.67, S.690 Ligand excluded by PLIP GOL.15: 3 residues within 4Å: Chain A: R.43 Chain B: N.242, I.244 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain A: T.140, H.141, V.149, K.150 Ligands: GOL.13 Ligand excluded by PLIP GOL.17: 3 residues within 4Å: Chain A: T.254, R.256, D.257 Ligand excluded by PLIP GOL.18: 3 residues within 4Å: Chain A: T.339, E.340, D.359 Ligand excluded by PLIP GOL.19: 8 residues within 4Å: Chain A: P.124, V.125, C.126, G.127, I.128, K.285, H.286, P.287 Ligand excluded by PLIP GOL.27: 6 residues within 4Å: Chain B: S.351, T.353, N.354, L.645, T.646, R.647 Ligand excluded by PLIP GOL.28: 6 residues within 4Å: Chain B: H.141, V.149, K.150, R.151, E.293, K.295 Ligand excluded by PLIP GOL.29: 5 residues within 4Å: Chain B: H.141, N.142, S.148, V.149, K.150 Ligand excluded by PLIP GOL.30: 4 residues within 4Å: Chain B: R.53, R.66, K.67, S.690 Ligand excluded by PLIP GOL.31: 4 residues within 4Å: Chain B: Y.380, G.381, D.382, F.644 Ligand excluded by PLIP GOL.32: 4 residues within 4Å: Chain B: L.544, Y.642, A.643, F.644 Ligand excluded by PLIP GOL.33: 2 residues within 4Å: Chain B: R.73, L.75 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.20: 6 residues within 4Å: Chain A: L.263, D.264, P.268 Chain B: Y.691, Q.694, M.696 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:L.263, H2O.1, H2O.17

2 x CDP: CYTIDINE-5'-DIPHOSPHATE(Non-covalent)

CDP.21: 13 residues within 4Å: Chain A: E.583, T.584, T.586, M.587, R.590, T.591, D.594, M.628, R.629, V.630, Q.631, E.632, A.638 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.583, A:Q.631, A:E.632 Water bridges: A:E.632, A:A.638 CDP.34: 11 residues within 4Å: Chain B: T.584, T.586, M.587, R.590, T.591, D.594, M.628, V.630, Q.631, E.632, A.638 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.590, B:D.594, B:Q.631, B:Q.631, B:E.632, B:E.632, B:E.632 Water bridges: B:A.638, B:A.638

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
A

B
B

RNA-dependent RNA polymerase

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