Research workbench
COVID-19 RNA-dependent RNA polymerase post-translocated catalytic complex
Analyse COVID-19 RNA-dependent RNA polymerase post-translocated catalytic complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BZF
- Type
- protein + RNA
- Length
- 1,219 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
- ZN
- Pockets
- 13 · best druggability 0.79
Structure
electron microscopy · 6 distinct chains · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 914 | 37% helix, 14% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 114 | 32% helix, 26% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 68 | 68% helix, 0% strand | P0DTD1 |
| D | Non-structural protein 8 | protein | 104 | 19% helix, 22% strand | P0DTD1 |
| F | RNA (31-mer) | rna | 10 | — | — |
| G | RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*CP*AP*CP*A)-3') | rna | 9 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 943 | 0.79 | 0.82 | 71 | empty |
| 2 | 106 | 0.77 | 0.97 | 20 | empty |
| 3 | 56 | 0.67 | 0.95 | 21 | empty |
| 4 | 429 | 0.64 | 0.78 | 41 | empty |
| 5 | 226 | 0.58 | 0.80 | 37 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2484 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1195 Ų buried · 6 hydrogen bonds · protein-protein
- A–F · 966 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–C · 888 Ų buried · 9 hydrogen bonds · protein-protein
- A–G · 642 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 7BZF · COVID-19 RNA-dependent RNA polymerase post-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 7BZF · PDBe 7BZF · UniProt P0DTD1
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