SMTL ID : 5tsn.1

Crystal structures of Norwalk virus polymerase bound to an RNA primer-template duplex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

2 x U- A- C- C- C- G- G- G: RNA (5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3')(Non-covalent)

U-A-C-C-C-G-G-G.1: 36 residues within 4Å: Chain A: T.116, R.126, N.128, K.166, R.182, L.184, D.242, W.246, D.247, S.300, G.301, T.305, S.306, N.309, Y.341, G.342, D.343, D.344, L.391, R.392, R.393, L.406, S.410, R.413, Q.414, R.419, Q.435, Q.439 Ligands: A-C-C-C-G-G-G.2, A-C-C-C-G-G-G.2, A-C-C-C-G-G-G.2, A-C-C-C-G-G-G.2, A-C-C-C-G-G-G.2, A-C-C-C-G-G-G.2, MN.3, MN.4 Protein-ligand interaction information (PLIP) not available U-A-C-C-C-G-G-G.2: 37 residues within 4Å: Chain A: S.23, K.25, K.27, T.117, S.118, K.127, A.164, L.165, K.166, D.167, L.184, W.185, G.186, S.187, M.192, K.207, V.217, G.218, M.219, N.220, G.301, V.302, P.303, C.304, Y.341, N.422, S.502, F.503, V.504, N.505 Ligands: U-A-C-C-C-G-G-G.1, U-A-C-C-C-G-G-G.1, U-A-C-C-C-G-G-G.1, U-A-C-C-C-G-G-G.1, U-A-C-C-C-G-G-G.1, U-A-C-C-C-G-G-G.1, U-A-C-C-C-G-G-G.1 Protein-ligand interaction information (PLIP) not available

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 6 residues within 4Å: Chain A: D.242, D.343, D.344 Ligands: U-A-C-C-C-G-G-G.1, U-A-C-C-C-G-G-G.1, MN.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.242, A:D.343, A:D.344, H2O.10 MN.4: 5 residues within 4Å: Chain A: D.242, Y.243, D.343 Ligands: U-A-C-C-C-G-G-G.1, MN.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.242, A:Y.243, A:D.343, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shaik, M.M. et al., Norovirus RNA-dependent RNA polymerase: A computational study of metal-binding preferences. Proteins (2017)

Release Date

2017-04-12

Peptides

Norwalk virus polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Norwalk virus polymerase

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