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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.56 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.242, Y.243, D.343 Ligands: URF.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.242, A:D.343, H2O.3 MG.10: 4 residues within 4Å: Chain B: D.242, Y.243, D.343 Ligands: URF.11 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.242, B:D.343, H2O.6, H2O.9

2 x URF: 5-FLUOROURACIL(Non-covalent)

URF.2: 5 residues within 4Å: Chain A: R.182, D.242, D.343, D.344 Ligands: MG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.344, A:D.344 Halogen bonds: A:R.182 URF.11: 6 residues within 4Å: Chain B: R.182, D.242, D.343, D.344, R.392 Ligands: MG.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.344

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

MN3.3: 4 residues within 4Å: Chain A: K.207, C.210, G.218 Ligands: MN3.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:K.207, A:C.210, H2O.1 MN3.4: 6 residues within 4Å: Chain A: K.207, E.208, T.209, C.210, I.211 Ligands: MN3.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.210, H2O.1, H2O.5 MN3.12: 3 residues within 4Å: Chain B: K.207, C.210 Ligands: MN3.13 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:K.207, B:C.210 MN3.13: 4 residues within 4Å: Chain B: E.208, C.210, I.211 Ligands: MN3.12 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.210

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

SO4.5: 5 residues within 4Å: Chain A: T.25, G.48, S.49, S.58, L.59 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.49, A:L.59 Water bridges: A:K.50 SO4.6: 4 residues within 4Å: Chain A: D.114, T.117, K.127, M.192 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.114, A:D.114, A:T.117 Water bridges: A:G.301 Salt bridges: A:K.127 SO4.7: 2 residues within 4Å: Chain A: H.146, N.149 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.149 Salt bridges: A:H.146 SO4.8: 3 residues within 4Å: Chain A: Y.17, D.289, Y.290 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.289, A:Y.290 SO4.9: 3 residues within 4Å: Chain A: T.325, V.327, E.352 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.352 SO4.14: 4 residues within 4Å: Chain B: G.48, S.49, S.58, L.59 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.49, B:S.49, B:L.59 SO4.15: 2 residues within 4Å: Chain B: H.146, N.149 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.149 Salt bridges: B:H.146 SO4.16: 5 residues within 4Å: Chain A: Q.334 Chain B: G.397, D.398, G.401, W.402 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 5 residues within 4Å: Chain B: T.8, Y.9, A.10, G.11, R.64 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.10, B:G.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, K.H. et al., Crystal structures and functional analysis of murine norovirus RNA-dependent RNA polymerase. To be Published

Release Date

2011-06-08

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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