SMTL ID : 1gx6.1

Hepatitis C Virus RNA polymerase in complex with UTP and manganese

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

6 x UTP: URIDINE 5'-TRIPHOSPHATE(Non-covalent)

UTP.1: 16 residues within 4Å: Chain A: R.158, L.159, D.220, T.221, C.223, F.224, D.225, S.282, T.287, D.318, D.319 Ligands: UTP.3, MN.4, MN.5, MN.6, MN.8 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:L.159, A:L.159, A:C.223, A:F.224, A:D.225, A:D.225, A:S.282 Water bridges: A:R.48, A:N.291, A:D.318, A:D.318 UTP.2: 10 residues within 4Å: Chain A: E.143, F.145, K.155, R.158, S.367, R.386, T.390, R.394 Ligands: MN.6, MN.7 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.367, A:T.390 Water bridges: A:C.366, A:S.367, A:R.386, A:R.386, A:T.390, A:R.394 Salt bridges: A:K.155, A:R.158, A:R.386, A:R.386, A:R.394, A:R.394 UTP.3: 7 residues within 4Å: Chain A: R.48, K.51, K.155, R.158 Ligands: UTP.1, MN.7, MN.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.158 Water bridges: A:R.48 Salt bridges: A:R.48, A:K.51, A:K.155 UTP.9: 16 residues within 4Å: Chain B: R.158, L.159, D.220, T.221, C.223, F.224, D.225, S.282, T.287, D.318, D.319 Ligands: UTP.11, MN.12, MN.13, MN.14, MN.16 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:L.159, B:L.159, B:C.223, B:F.224, B:D.225, B:D.225, B:S.282 Water bridges: B:R.48, B:N.291, B:D.318, B:D.318 UTP.10: 10 residues within 4Å: Chain B: E.143, F.145, K.155, R.158, S.367, R.386, T.390, R.394 Ligands: MN.14, MN.15 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.367, B:T.390 Water bridges: B:C.366, B:S.367, B:R.386, B:R.386, B:T.390, B:R.394 Salt bridges: B:K.155, B:R.158, B:R.386, B:R.386, B:R.394, B:R.394 UTP.11: 7 residues within 4Å: Chain B: R.48, K.51, K.155, R.158 Ligands: UTP.9, MN.15, MN.16 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.158 Water bridges: B:R.48 Salt bridges: B:R.48, B:K.51, B:K.155

10 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.4: 5 residues within 4Å: Chain A: D.220, T.221, D.318 Ligands: UTP.1, MN.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.220, A:T.221, A:D.318, H2O.19 MN.5: 5 residues within 4Å: Chain A: D.220, D.318, D.319 Ligands: UTP.1, MN.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.220, A:D.318, A:D.319, H2O.19 MN.6: 4 residues within 4Å: Chain A: S.367 Ligands: UTP.1, UTP.2, MN.7 No protein-ligand interaction detected (PLIP) MN.7: 4 residues within 4Å: Chain A: R.158 Ligands: UTP.2, UTP.3, MN.6 No protein-ligand interaction detected (PLIP) MN.8: 2 residues within 4Å: Ligands: UTP.1, UTP.3 No protein-ligand interaction detected (PLIP) MN.12: 5 residues within 4Å: Chain B: D.220, T.221, D.318 Ligands: UTP.9, MN.13 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.220, B:T.221, B:D.318, H2O.38 MN.13: 5 residues within 4Å: Chain B: D.220, D.318, D.319 Ligands: UTP.9, MN.12 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.220, B:D.318, B:D.319, H2O.38 MN.14: 4 residues within 4Å: Chain B: S.367 Ligands: UTP.9, UTP.10, MN.15 No protein-ligand interaction detected (PLIP) MN.15: 4 residues within 4Å: Chain B: R.158 Ligands: UTP.10, UTP.11, MN.14 No protein-ligand interaction detected (PLIP) MN.16: 2 residues within 4Å: Ligands: UTP.9, UTP.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bressanelli, S. et al., A Structural Analysis of the Hepatitis C Virus RNA Polymerase in Complex with Ribonucleotides. J.Virol. (2002)

Release Date

2002-04-10

Peptides

RNA-DIRECTED RNA POLYMERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

RNA-DIRECTED RNA POLYMERASE