SMTL ID : 4wtl.1

CRYSTAL STRUCTURE OF HCV NS5B GENOTYPE 2A JFH-1 ISOLATE WITH S15G E86Q E87Q C223H V321I MUTATIONS IN COMPLEX WITH RNA TEMPLATE 5'-UACC, RNA PRIMER 5'-PGG, MN2+, AND UDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x U- A- C- C: RNA TEMPLATE UACC(Non-covalent)

U-A-C-C.1: 21 residues within 4Å: Chain A: P.95, H.97, S.98, A.99, K.143, I.162, Y.164, R.170, K.174, Q.182, F.195, S.284, G.285, V.286, L.287, T.289, Y.450, G.451 Ligands: G-G.2, G-G.2, UDP.6 Protein-ligand interaction information (PLIP) not available

1 x G- G: RNA PRIMER GG(Non-covalent)

G-G.2: 16 residues within 4Å: Chain A: F.195, T.289, S.290, G.319, D.320, D.321, C.368, S.369, R.388, R.396, Y.450 Ligands: U-A-C-C.1, U-A-C-C.1, U-A-C-C.1, MN.3, UDP.6 Protein-ligand interaction information (PLIP) not available

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

MN.3: 6 residues within 4Å: Chain A: D.222, D.320, D.321 Ligands: G-G.2, MN.4, UDP.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.222, A:D.320, A:D.321, H2O.7 MN.4: 5 residues within 4Å: Chain A: D.222, T.223, D.320 Ligands: MN.3, UDP.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.222, A:T.223, A:D.320, H2O.7

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 6 residues within 4Å: Chain A: G.377, P.378, R.379, G.380, R.381, R.383 Ligand excluded by PLIP

1 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.6: 16 residues within 4Å: Chain A: R.50, K.143, R.160, D.222, T.223, H.225, F.226, D.227, S.284, T.289, N.293, D.320 Ligands: U-A-C-C.1, G-G.2, MN.3, MN.4 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:R.160, A:H.225, A:F.226, A:D.227, A:D.227, A:D.227, A:S.284, A:N.293 Water bridges: A:R.50, A:R.50, A:R.50, A:R.50, A:K.143, A:K.143, A:R.160, A:T.223, A:H.225 Salt bridges: A:R.50, A:R.160, A:R.160

1 x PG6: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE(Non-covalent)

PG6.7: 7 residues within 4Å: Chain A: K.102, Y.103, P.137, T.139, F.269, N.270, G.273 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.103

1 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.8: 2 residues within 4Å: Chain A: W.210, P.216 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.360

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Appleby, T.C. et al., Structural basis for RNA replication by the hepatitis C virus polymerase. Science (2015)

Release Date

2015-02-11

Peptides

RNA-directed RNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA-directed RNA polymerase

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