MolNFT v1 · #174662 · protein + RNA
COVID-19 RNA-dependent RNA polymerase pre-translocated catalytic complex
7C2K · RNA-directed RNA polymerase: “COVID-19 RNA-dependent RNA polymerase pre-translocated catalytic complex”. Electron microscopy, 2 ligands (F86, ZN), 18 pockets (best druggability 0.81). MolNFT v1 #174662 on GenesisL1: 3D structure…
- PDB
- 7C2K
- Type
- protein + RNA
- Length
- 1,287 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase; Non-structural protein 8; Non-structural protein 7; RNA…
- EC
- 2.7.7.48
- UniProt
- P0DTD1
- Ligands
- F86, ZN
- Pockets
- 18 · best druggability 0.81
Structure
electron microscopy · 6 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 927 | 43% helix, 16% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 117 | 38% helix, 25% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 73 | 70% helix, 0% strand | P0DTD1 |
| D | Non-structural protein 8 | protein | 139 | 40% helix, 22% strand | P0DTD1 |
| F | RNA (29-mer) | rna | 20 | — | — |
| G | RNA (5'- R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*CP*AP*CP*AP*GP*G*(F86)P*G)-3') | rna | 11 | — | — |
Ligands and binding sites
- F86 · [(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-F][1, 2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate · ligand · chains A, F, G
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 498 | 0.81 | 0.89 | 64 | F86 |
| 2 | 109 | 0.72 | 0.94 | 37 | empty |
| 3 | 279 | 0.70 | 0.84 | 31 | empty |
| 4 | 425 | 0.69 | 0.81 | 53 | empty |
| 5 | 358 | 0.68 | 0.81 | 48 | empty |
Interfaces
9 interfaces between chains.
- A–B · 2543 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1397 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 1158 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–C · 894 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 870 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7C2K · COVID-19 RNA-dependent RNA polymerase pre-translocated catalytic complex · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0DTD1
- Elsewhere: RCSB PDB 7C2K · PDBe 7C2K · UniProt P0DTD1
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