SMTL ID : 3avx.1

Structure of viral RNA polymerase complex 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

monomer

Ligands

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

G-G-G-U-C-C-A-U-C.1: 34 residues within 4Å: Chain A: S.849, G.850, R.858, H.862, P.863, Q.948, F.1023, Y.1051, G.1052, D.1053, D.1054, C.1091, G.1092, Y.1105, R.1107, L.1118, N.1122, D.1163, D.1190, Y.1205, N.1243, P.1244, S.1248, S.1250 Chain B: G.4, A.5, U.6, G.7, G.8, A.9, C.10, C.11, C.12 Ligands: GH3.2 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:V.906, A:I.916 Hydrogen bonds: A:R.573, A:T.620, A:R.662, A:R.662, A:G.664, A:R.666, A:S.849, A:S.849, A:G.851, A:A.852, A:N.856, A:N.857, A:R.858, A:R.935, A:R.935, A:Q.948, A:Y.1161, A:Q.1257 Water bridges: A:K.866, A:Q.948, A:N.1019, A:N.1019, A:G.1020, A:E.1024 Salt bridges: A:R.847, A:R.858, A:R.935

1 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.971, A.972, S.973, M.1017, G.1018, E.1026, D.1053, N.1077 Chain B: C.3, G.4 Ligands: G-G-G-U-C-C-A-U-C.1, CA.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.972 Hydrogen bonds: A:S.970, A:A.972, A:S.973, A:S.973 Water bridges: A:S.973, A:G.1018 Salt bridges: A:K.908, A:K.908, A:K.908, A:R.914, A:R.914

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.968, L.969, D.1053 Ligands: GH3.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.968, A:L.969, A:D.1053 CA.4: 3 residues within 4Å: Chain A: D.968, D.1054, E.1089 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.1054, A:E.1089

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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