SMTL ID : 3sfu.1 (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: 9 residues within 4Å: Chain A: D.247, S.300, T.305, T.306, N.309, Y.341, G.342, D.343, D.344 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.305, A:T.306, A:T.306, A:N.309, A:D.343, A:D.343, A:D.344 RBV.21: 9 residues within 4Å: Chain B: D.247, S.300, T.305, T.306, N.309, Y.341, G.342, D.343, D.344 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.306, B:N.309, B:D.343, B:D.343, B:D.343

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

SO4.2: 3 residues within 4Å: Chain A: K.115, W.131, G.133 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: T.145, H.146, N.149 Ligand excluded by PLIP SO4.4: 7 residues within 4Å: Chain A: A.233, F.235, H.238, Q.383, T.384, L.385, W.402 Ligand excluded by PLIP SO4.5: 5 residues within 4Å: Chain A: K.26, H.423, Q.424, N.425, E.428 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: Y.243, T.244, R.245 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: S.58, Q.60, R.64 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: G.154, K.155, S.156 Ligand excluded by PLIP SO4.9: 2 residues within 4Å: Chain A: R.405 Ligands: GOL.15 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain B: K.115, W.131, G.133 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain B: T.145, H.146, N.149 Ligand excluded by PLIP SO4.24: 7 residues within 4Å: Chain B: A.233, F.235, H.238, Q.383, T.384, L.385, W.402 Ligand excluded by PLIP SO4.25: 5 residues within 4Å: Chain B: K.26, H.423, Q.424, N.425, E.428 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain B: Y.243, T.244, R.245 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain B: S.58, Q.60, R.64 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain B: G.154, K.155, S.156 Ligand excluded by PLIP SO4.29: 2 residues within 4Å: Chain B: R.405 Ligands: GOL.35 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 4 residues within 4Å: Chain A: D.240, D.344, E.345, S.389 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.240, A:D.344, A:E.345, A:S.389, H2O.102 MG.30: 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.281

20 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 4 residues within 4Å: Chain A: S.24, T.25, K.26, N.422 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain A: G.397, D.398, W.402 Chain B: Q.334 Ligand excluded by PLIP GOL.13: 3 residues within 4Å: Chain A: M.441, P.476, W.484 Ligand excluded by PLIP GOL.14: 3 residues within 4Å: Chain A: S.220, M.221, N.222 Ligand excluded by PLIP GOL.15: 5 residues within 4Å: Chain A: R.405, D.407, R.408, H.450 Ligands: SO4.9 Ligand excluded by PLIP GOL.16: 3 residues within 4Å: Chain A: T.325, L.351, E.352 Ligand excluded by PLIP GOL.17: 10 residues within 4Å: Chain A: R.93, F.212, N.213, P.214, R.216, R.231, M.333, S.336, E.337, F.338 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain A: P.100, Q.101, L.265, S.266, P.267 Ligand excluded by PLIP GOL.19: 6 residues within 4Å: Chain A: W.104, S.112, G.200, C.203, D.204, P.303 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain A: L.2, P.3, A.15, D.16, Y.17 Ligand excluded by PLIP GOL.31: 4 residues within 4Å: Chain B: S.24, T.25, K.26, N.422 Ligand excluded by PLIP GOL.32: 4 residues within 4Å: Chain A: Q.334 Chain B: G.397, D.398, W.402 Ligand excluded by PLIP GOL.33: 3 residues within 4Å: Chain B: M.441, P.476, W.484 Ligand excluded by PLIP GOL.34: 3 residues within 4Å: Chain B: S.220, M.221, N.222 Ligand excluded by PLIP GOL.35: 5 residues within 4Å: Chain B: R.405, D.407, R.408, H.450 Ligands: SO4.29 Ligand excluded by PLIP GOL.36: 3 residues within 4Å: Chain B: T.325, L.351, E.352 Ligand excluded by PLIP GOL.37: 10 residues within 4Å: Chain B: R.93, F.212, N.213, P.214, R.216, R.231, M.333, S.336, E.337, F.338 Ligand excluded by PLIP GOL.38: 5 residues within 4Å: Chain B: P.100, Q.101, L.265, S.266, P.267 Ligand excluded by PLIP GOL.39: 6 residues within 4Å: Chain B: W.104, S.112, G.200, C.203, D.204, P.303 Ligand excluded by PLIP GOL.40: 5 residues within 4Å: Chain B: L.2, P.3, A.15, D.16, Y.17 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
A

B
A

RNA polymerase

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