SMTL ID : 4wtj.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

A-U-C-C.1: 24 residues within 4Å: Chain A: C.16, G.17, P.95, H.97, S.98, A.99, M.141, K.143, I.162, Y.164, R.170, K.174, Q.182, S.284, G.285, V.286, L.287, S.290, Y.450, G.451, V.555 Ligands: G-G.2, G-G.2, ADP.6 Protein-ligand interaction information (PLIP) not available

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

G-G.2: 17 residues within 4Å: Chain A: F.195, T.289, S.290, C.318, G.319, D.320, D.321, C.368, S.369, R.388, Q.416, Y.417, Y.450 Ligands: A-U-C-C.1, A-U-C-C.1, MN.3, ADP.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, ADP.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.6 MN.4: 5 residues within 4Å: Chain A: D.222, T.223, D.320 Ligands: MN.3, ADP.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: 5 residues within 4Å: Chain A: G.377, P.378, R.379, G.380, R.381 Ligand excluded by PLIP

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.6: 18 residues within 4Å: Chain A: R.50, K.143, R.160, I.162, D.222, T.223, H.225, F.226, D.227, S.284, T.289, N.293, D.320 Ligands: A-U-C-C.1, A-U-C-C.1, G-G.2, MN.3, MN.4 15 PLIP interactions: 15 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:N.293 Water bridges: A:R.50, A:E.145, A:R.160, A:R.160, A:D.227 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: 6 residues within 4Å: Chain A: Y.103, P.137, T.139, F.269, N.270, G.273 No protein-ligand interaction detected (PLIP)

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

B3P.8: 4 residues within 4Å: Chain A: W.210, K.213, K.214, P.216 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.215, A:Y.360

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.9: 7 residues within 4Å: Chain A: W.8, G.10, A.11, L.12, S.48, A.51, K.52 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.48 Water bridges: A:G.10

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.10: 4 residues within 4Å: Chain A: E.212, K.213, A.312, E.327 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.212, A:K.213, A:E.327, A:E.327

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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