SMTL ID : 6xqb.1

SARS-CoV-2 RdRp/RNA complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-1-mer

Ligands

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

G-G-G-C-C-C-A.1: 27 residues within 4Å: Chain A: N.497, L.499, R.514, T.688, A.689, L.759, S.760, D.761, D.762, C.814, S.815, Q.816, R.837, A.841, I.848, L.855, E.858, R.859, S.862, L.863 Ligands: G-U-G-G-G-C-C-C.2, G-U-G-G-G-C-C-C.2, G-U-G-G-G-C-C-C.2, G-U-G-G-G-C-C-C.2, G-U-G-G-G-C-C-C.2, G-U-G-G-G-C-C-C.2, G-U-G-G-G-C-C-C.2 Protein-ligand interaction information (PLIP) not available G-G-G-C-C-C-A.2: 30 residues within 4Å: Chain A: N.498, K.501, S.502, V.558, R.570, L.577, K.578, A.581, R.584, I.590, G.591, S.593, F.595, Y.596, S.683, G.684, D.685, A.686, T.687, T.688, Y.690, E.858, Y.916 Ligands: G-G-G-C-C-C-A.1, G-G-G-C-C-C-A.1, G-G-G-C-C-C-A.1, G-G-G-C-C-C-A.1, G-G-G-C-C-C-A.1, G-G-G-C-C-C-A.1, G-G-G-C-C-C-A.1 Protein-ligand interaction information (PLIP) not available

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: T.294, H.296, C.302, L.303, C.307, C.311 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.302, A:C.307, A:C.311 ZN.4: 4 residues within 4Å: Chain A: C.488, H.643, C.646, C.647 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.488, A:H.643, A:C.646, A:C.647

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Chain A: W.618, D.619, D.762, A.763, E.812 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:W.618, A:E.812

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, B. et al., Structure of SARS-CoV-2 RdRp/RNA complex at 3.4 Angstroms resolution. To Be Published

Release Date

2020-07-29

Peptides

RNA-directed RNA polymerase: A
Non-structural protein 8: BD
Non-structural protein 7: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

C
C

RNA-directed RNA polymerase

Non-structural protein 8

Non-structural protein 7