SMTL ID : 3sfu.2 (1 other biounit)

crystal structure of murine norovirus RNA dependent RNA polymerase in complex with ribavirin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x RBV: 1-(beta-D-ribofuranosyl)-1H-1,2,4-triazole-3-carboxamide(Non-covalent)

RBV.1: 10 residues within 4Å: Chain A: D.247, T.305, T.306, N.309, Y.341, G.342, D.343, D.344, L.391, R.392 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.306, A:N.309 Water bridges: A:R.182, A:R.392, A:R.392 RBV.19: 13 residues within 4Å: Chain B: K.166, R.182, L.183, L.184, D.247, L.298, S.300, T.305, T.306, N.309, Y.341, G.342, D.343 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.182, B:D.247, B:N.309, B:D.343 Water bridges: B:W.185, B:S.300

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

SO4.2: 3 residues within 4Å: Chain A: T.145, H.146, N.149 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: Y.243, T.244, R.245 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: K.26, N.422, H.423, Q.424 Ligand excluded by PLIP SO4.5: 2 residues within 4Å: Chain A: K.155, S.156 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: D.407, R.408, H.450 Ligand excluded by PLIP SO4.7: 6 residues within 4Å: Chain A: G.48, S.49, P.57, S.58, L.59, Q.60 Ligand excluded by PLIP SO4.8: 1 residues within 4Å: Chain A: R.405 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain B: T.145, H.146, N.149 Ligand excluded by PLIP SO4.21: 2 residues within 4Å: Chain B: T.244, R.245 Ligand excluded by PLIP SO4.23: 1 residues within 4Å: Chain B: R.405 Ligand excluded by PLIP SO4.25: 5 residues within 4Å: Chain A: A.233, N.234 Chain B: A.233, N.234 Ligands: GOL.34 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain B: K.155, S.156 Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Chain B: G.48, S.49, S.58, L.59, Q.60 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain B: K.115, W.131, G.133 Ligand excluded by PLIP SO4.29: 1 residues within 4Å: Chain B: R.245 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain B: V.356, R.363, G.377, P.378 Ligand excluded by PLIP SO4.31: 5 residues within 4Å: Chain B: D.240, R.371, A.372, L.379, E.380 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain B: Y.237, R.381, Q.383 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain B: D.407, R.408, H.450 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 4 residues within 4Å: Chain A: D.240, D.344, E.345, S.389 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.240, A:D.344, A:E.345, A:S.389 MG.22: 4 residues within 4Å: Chain B: D.240, D.344, E.345, S.389 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.240, B:D.344, B:E.345, B:S.389, H2O.9

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 3 residues within 4Å: Chain A: S.220, M.221, N.222 Ligand excluded by PLIP GOL.11: 4 residues within 4Å: Chain A: I.82, V.322, R.326, D.328 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain A: S.24, T.25, K.26, N.422 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain A: V.324, R.326, D.354, K.357 Ligand excluded by PLIP GOL.14: 2 residues within 4Å: Chain A: P.79, Q.80 Ligand excluded by PLIP GOL.15: 2 residues within 4Å: Chain A: T.244, R.245 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain A: D.398, G.401, W.402 Chain B: R.231, N.234, F.235 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain A: P.100, Q.101, F.202, L.265, S.266, P.267 Ligand excluded by PLIP GOL.18: 4 residues within 4Å: Chain A: E.335, N.350, L.351, E.352 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain B: Q.386, G.397, D.398, W.402 Ligands: GOL.34 Ligand excluded by PLIP GOL.34: 11 residues within 4Å: Chain A: N.234 Chain B: A.233, F.235, H.238, Q.383, T.384, L.385, Q.386, W.402 Ligands: GOL.24, SO4.25 Ligand excluded by PLIP GOL.35: 2 residues within 4Å: Chain B: G.7, T.8 Ligand excluded by PLIP GOL.36: 4 residues within 4Å: Chain B: M.219, S.220, M.221, N.222 Ligand excluded by PLIP GOL.37: 4 residues within 4Å: Chain B: S.24, T.25, K.26, N.422 Ligand excluded by PLIP GOL.38: 5 residues within 4Å: Chain B: Q.143, H.146, A.147, D.188, G.190 Ligand excluded by PLIP GOL.39: 8 residues within 4Å: Chain A: Q.399 Chain B: R.93, P.214, W.314, M.333, S.336, E.337, F.338 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alam, I. et al., Crystal structures of murine norovirus-1 RNA-dependent RNA polymerase in complex with 2-thiouridine or ribavirin. Virology (2012)

Release Date

2012-05-09

Peptides

RNA polymerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

RNA polymerase

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