SMTL ID : 3avt.1

Structure of viral RNA polymerase complex 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

monomer

Ligands

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

G-C-C-A.1: 24 residues within 4Å: Chain A: R.847, S.849, G.851, A.852, N.857, R.858, T.905, V.906, P.907, I.916, A.917, I.918, M.924, L.928, R.935, L.945, Q.948, M.1017, G.1018, N.1019, F.1023, Y.1051 Ligands: GH3.2, GH3.5 Protein-ligand interaction information (PLIP) not available

2 x GH3: 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GH3.2: 17 residues within 4Å: Chain A: K.908, R.914, D.968, L.969, S.970, A.972, S.973, M.1017, G.1018, E.1026, D.1053, N.1077 Ligands: G-C-C-A.1, G-C-C-A.1, CA.3, CA.4, GH3.5 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:A.972, A:S.973, A:S.973, A:M.1017, A:N.1077 Salt bridges: A:K.908, A:K.908, A:R.914, A:R.914, A:K.1080 GH3.5: 13 residues within 4Å: Chain A: Q.948, F.1023, Y.1051, G.1052, D.1053, D.1054, E.1089, C.1091, G.1092 Ligands: G-C-C-A.1, G-C-C-A.1, GH3.2, CA.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.948, A:D.1053, A:D.1053, A:G.1092 Water bridges: A:K.772

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.968, L.969, S.970, D.1053 Ligands: GH3.2, CA.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.968, A:L.969 CA.4: 6 residues within 4Å: Chain A: D.968, D.1053, D.1054 Ligands: GH3.2, CA.3, GH3.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.968, A:D.1054

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takeshita, D. et al., Molecular basis for RNA polymerization by Q beta replicase. Nat.Struct.Mol.Biol. (2012)

Release Date

2012-01-18

Peptides

Elongation factor Ts, Elongation factor Tu, LINKER, Q beta replicase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Elongation factor Ts, Elongation factor Tu, LINKER, Q beta replicase

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