SMTL ID : 4wta.1

CRYSTAL STRUCTURE OF HCV NS5B GENOTYPE 2A JFH-1 ISOLATE WITH S15G E86Q E87Q C223H V321I MUTATIONS AND DELTA8 BETA HAIRPIN LOOP DELETION IN COMPLEX WITH UDP, MN2+ AND SYMMETRICAL PRIMER TEMPLATE 5'-CAAAAUUU

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

2 x C- A- A- A- A- U- U- U: RNA PRIMER TEMPLATE CAAAAUUU(Non-covalent)

C-A-A-A-A-U-U-U.1: 30 residues within 4Å: Chain A: P.95, S.98, A.99, K.143, I.162, Y.164, R.170, K.174, Y.178, Q.182, F.195, Y.197, S.198, P.199, S.284, G.285, V.286, L.287, S.290, I.415, G.447, V.448, I.456, L.460 Ligands: A-A-A-U-U-U.2, A-A-A-U-U-U.2, A-A-A-U-U-U.2, A-A-A-U-U-U.2, A-A-A-U-U-U.2, UDP.7 Protein-ligand interaction information (PLIP) not available C-A-A-A-A-U-U-U.2: 26 residues within 4Å: Chain A: H.97, K.143, D.222, S.290, C.318, G.319, D.320, D.321, C.368, S.369, R.388, R.396, N.408, S.409, G.412, N.413, Q.416, G.446 Ligands: C-A-A-A-A-U-U-U.1, C-A-A-A-A-U-U-U.1, C-A-A-A-A-U-U-U.1, C-A-A-A-A-U-U-U.1, C-A-A-A-A-U-U-U.1, C-A-A-A-A-U-U-U.1, MN.3, UDP.7 Protein-ligand interaction information (PLIP) not available

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

MN.3: 6 residues within 4Å: Chain A: D.222, D.320, D.321 Ligands: A-A-A-U-U-U.2, MN.4, UDP.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.222, A:D.320, A:D.321, H2O.1 MN.4: 5 residues within 4Å: Chain A: D.222, T.223, D.320 Ligands: MN.3, UDP.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.222, A:T.223, A:D.320, H2O.1 MN.5: 3 residues within 4Å: Chain A: E.239, Q.243, H.256 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.239, A:H.256

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

CL.6: 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.7: 17 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: C-A-A-A-A-U-U-U.1, C-A-A-A-A-U-U-U.1, A-A-A-U-U-U.2, MN.3, MN.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.160, A:H.225, A:H.225, A:F.226, A:D.227, A:D.227, A:D.227, A:S.284, A:N.293 Water bridges: A:D.222 Salt bridges: A:R.50, A:R.160, A:R.160

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

Related Entries With Identical Sequence