SMTL ID : 6k32.1

RdRp complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.20 Å

Oligo State

hetero-1-1-1-3-1-mer

Ligands

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

U-U-A-C-U.1: 23 residues within 4Å: Chain A: F.416, S.421, P.422, R.445, V.473, R.483, I.485, S.486, G.487, L.488, Y.500, S.635, G.636, A.638, T.640, S.641, E.741, D.742, T.743, Y.1079 Ligands: 3PO-A-G.2, 3PO-A-G.2, UTP.8 Protein-ligand interaction information (PLIP) not available

1 x 3PO- A- G: RNA (5'-D(*(3PO))-R(*AP*G)-3'(Non-covalent)

3PO-A-G.2: 18 residues within 4Å: Chain A: T.640, L.674, G.675, D.676, D.677, L.719, Q.720, R.734, I.735, R.766, H.1080, K.1081, R.1142 Ligands: U-U-A-C-U.1, U-U-A-C-U.1, U-U-A-C-U.1, MG.7, UTP.8 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.734 Salt bridges: A:R.766, A:H.1080, A:H.1080, A:H.1080, A:K.1081, A:R.1142, A:R.1142

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: D.543, V.544, A.545, D.676 Ligands: MG.7, UTP.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.543, A:D.676, A:D.676 MG.7: 5 residues within 4Å: Chain A: D.676, D.677 Ligands: 3PO-A-G.2, MG.3, UTP.8 No protein-ligand interaction detected (PLIP)

1 x MG7: 7-METHYLGUANOSINE(Covalent)

MG7.4: 7 residues within 4Å: Chain A: R.33, Y.180, S.182, P.183, S.184, Q.185 Ligands: DPO.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.33, A:S.184, A:S.184, A:S.184, A:Q.185

1 x DPO: DIPHOSPHATE(Non-covalent)

DPO.5: 6 residues within 4Å: Chain A: D.140, R.143, P.183, R.787 Ligands: MG7.4, A2M.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.140, A:D.140, A:R.787 Salt bridges: A:R.143

1 x A2M: 2'-O-methyladenosine 5'-(dihydrogen phosphate)(Non-covalent)

A2M.6: 5 residues within 4Å: Chain A: P.183, T.789, S.791, L.823 Ligands: DPO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.789, A:T.789

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

UTP.8: 19 residues within 4Å: Chain A: R.475, Q.477, R.480, R.481, R.483, D.543, V.544, A.545, G.546, M.547, D.548, T.640, H.644, G.675, D.676 Ligands: U-U-A-C-U.1, 3PO-A-G.2, MG.3, MG.7 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:R.483, A:R.483, A:V.544, A:V.544, A:A.545, A:M.547, A:D.548, A:T.640, A:H.644 Salt bridges: A:K.246, A:R.480, A:R.480, A:R.480, A:R.481

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, X. et al., Structure of RdRps Within a Transcribing dsRNA Virus Provides Insights Into the Mechanisms of RNA Synthesis. J.Mol.Biol. (2020)

Release Date

2019-11-20

Peptides

RNA-dependent RNA polymerase: A
Viral structural protein 4: B
VP1: C
VP1: DEF
VP1: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

RNA-dependent RNA polymerase

Viral structural protein 4

VP1

VP1

VP1