SMTL ID : 3sfg.1 (1 other biounit)

crystal structure of murine norovirus RNA dependent RNA polymerase in complex with 2thiouridine(2TU)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

homo-dimer

Ligands

2 x 2TU: 1-(beta-D-ribofuranosyl)-2-thioxo-2,3-dihydropyrimidin-4(1H)-one(Non-covalent)

2TU.1: 9 residues within 4Å: Chain A: L.184, D.247, L.298, S.300, T.305, T.306, N.309, Y.341, D.343 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.309, A:D.343, A:D.343, A:D.343 2TU.24: 9 residues within 4Å: Chain B: L.184, D.247, L.298, S.300, T.305, T.306, N.309, Y.341, D.343 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.309, B:D.343, B:D.343

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

SO4.2: 3 residues within 4Å: Chain A: Y.243, T.244, R.245 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: T.145, H.146, N.149 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: K.115, W.131, G.133 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain A: R.371, E.380, R.381, R.382 Ligand excluded by PLIP SO4.6: 2 residues within 4Å: Chain A: R.483 Chain B: P.100 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: P.79, Q.80, E.81 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain A: C.87, D.88, E.91, R.257, I.261 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain A: M.28, L.165, K.166, D.167, L.184 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain A: D.407, R.408, H.450 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain B: Y.243, T.244, R.245 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain B: T.145, H.146, N.149 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain B: K.115, W.131, G.133 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain B: R.371, E.380, R.381, R.382 Ligand excluded by PLIP SO4.29: 2 residues within 4Å: Chain A: P.100 Chain B: R.483 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain B: P.79, Q.80, E.81 Ligand excluded by PLIP SO4.31: 5 residues within 4Å: Chain B: C.87, D.88, E.91, R.257, I.261 Ligand excluded by PLIP SO4.32: 5 residues within 4Å: Chain B: M.28, L.165, K.166, D.167, L.184 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain B: D.407, R.408, H.450 Ligand excluded by PLIP

24 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: 5 residues within 4Å: Chain A: D.114, T.117, S.118, K.127, M.192 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain A: T.8, Y.9, A.10, R.64 Ligand excluded by PLIP GOL.14: 3 residues within 4Å: Chain A: S.220, M.221, N.222 Ligand excluded by PLIP GOL.15: 7 residues within 4Å: Chain A: T.25, G.48, S.49, K.50, P.57, S.58, L.59 Ligand excluded by PLIP GOL.16: 2 residues within 4Å: Chain A: K.155, S.156 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain A: F.106, C.110, S.134, A.135, F.136 Ligand excluded by PLIP GOL.18: 9 residues within 4Å: Chain A: D.398, Q.399, F.400, G.401, W.402 Chain B: R.231, N.234, F.235, E.337 Ligand excluded by PLIP GOL.19: 6 residues within 4Å: Chain A: P.21, S.118, G.120, H.124, T.162, G.186 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain A: K.26, N.422, H.423, Q.424 Ligand excluded by PLIP GOL.21: 6 residues within 4Å: Chain A: R.4, S.6, I.14, A.15, D.16, Y.17 Ligand excluded by PLIP GOL.22: 3 residues within 4Å: Chain A: R.381, R.382, Q.383 Ligand excluded by PLIP GOL.34: 4 residues within 4Å: Chain B: S.24, T.25, K.26, N.422 Ligand excluded by PLIP GOL.35: 5 residues within 4Å: Chain B: D.114, T.117, S.118, K.127, M.192 Ligand excluded by PLIP GOL.36: 4 residues within 4Å: Chain B: T.8, Y.9, A.10, R.64 Ligand excluded by PLIP GOL.37: 3 residues within 4Å: Chain B: S.220, M.221, N.222 Ligand excluded by PLIP GOL.38: 7 residues within 4Å: Chain B: T.25, G.48, S.49, K.50, P.57, S.58, L.59 Ligand excluded by PLIP GOL.39: 2 residues within 4Å: Chain B: K.155, S.156 Ligand excluded by PLIP GOL.40: 5 residues within 4Å: Chain B: F.106, C.110, S.134, A.135, F.136 Ligand excluded by PLIP GOL.41: 9 residues within 4Å: Chain A: R.231, N.234, F.235, E.337 Chain B: D.398, Q.399, F.400, G.401, W.402 Ligand excluded by PLIP GOL.42: 6 residues within 4Å: Chain B: P.21, S.118, G.120, H.124, T.162, G.186 Ligand excluded by PLIP GOL.43: 4 residues within 4Å: Chain B: K.26, N.422, H.423, Q.424 Ligand excluded by PLIP GOL.44: 6 residues within 4Å: Chain B: R.4, S.6, I.14, A.15, D.16, Y.17 Ligand excluded by PLIP GOL.45: 3 residues within 4Å: Chain B: R.381, R.382, Q.383 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.23: 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.3 MG.46: 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.11

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

Related Entries With Identical Sequence