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

Crystal structures and functional analysis of murine norovirus RNA-dependent RNA polymerase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: D.407, R.408, H.450 Ligand excluded by PLIP SO4.2: 3 residues within 4Å: Chain A: G.154, K.155, S.156 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: D.114, T.117, K.127, M.192 Ligand excluded by PLIP SO4.4: 5 residues within 4Å: Chain A: K.26, N.422, H.423, Q.424, E.428 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: T.145, H.146, N.149 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: I.82, V.322, R.326, D.328 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain A: T.244, R.245 Ligand excluded by PLIP SO4.8: 6 residues within 4Å: Chain A: G.48, S.49, P.57, S.58, L.59, Q.60 Ligand excluded by PLIP SO4.9: 2 residues within 4Å: Chain A: P.79, Q.80 Ligand excluded by PLIP SO4.15: 2 residues within 4Å: Chain B: H.146, N.149 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain B: V.396, R.405 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain B: Y.243, T.244, R.245 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain B: K.155, S.156 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain B: G.48, S.49, S.58, L.59 Ligand excluded by PLIP SO4.20: 2 residues within 4Å: Chain B: T.244, R.245 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain B: D.407, R.408, A.409, H.450 Ligand excluded by PLIP

2 x MN3: MANGANESE (III) ION(Non-covalent)

MN3.10: 2 residues within 4Å: Chain A: D.240, D.344 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.344, H2O.4, H2O.5 MN3.22: 3 residues within 4Å: Chain B: D.240, D.344, S.389 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.344, H2O.10

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 4 residues within 4Å: Chain A: S.24, T.25, K.26, N.422 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.25, A:T.25, A:N.422 GOL.12: 4 residues within 4Å: Chain A: T.325, L.351, E.352 Ligands: GOL.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.352 GOL.13: 4 residues within 4Å: Chain A: E.335, N.350, L.351 Ligands: GOL.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.335 Water bridges: A:N.350 GOL.14: 3 residues within 4Å: Chain A: R.182, T.244, R.245 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.245 Water bridges: A:Y.243, A:D.247, A:D.343 GOL.23: 4 residues within 4Å: Chain B: S.24, T.25, K.26, N.422 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.25, B:N.422 GOL.24: 3 residues within 4Å: Chain B: T.8, A.10, G.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.10, B:G.11 GOL.25: 5 residues within 4Å: Chain B: N.422, H.423, Q.424, N.425, E.428 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.26, B:Q.424, B:N.425, B:E.428

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, J.H. et al., Crystal structures of murine norovirus-1 RNA-dependent RNA polymerase. J.Gen.Virol. (2011)

Release Date

2011-12-21

Peptides

RNA dependent RNA polymerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

RNA dependent RNA polymerase

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