Research workbench
Structure of COVID-19 RNA-dependent RNA polymerase bound to penciclovir.
Analyse Structure of COVID-19 RNA-dependent RNA polymerase bound to penciclovir. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DOI
- Type
- protein + RNA
- Length
- 1,222 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
- POP, HCU, MG, ZN
- Pockets
- 11 · best druggability 0.81
Structure
electron microscopy · 6 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 906 | 41% helix, 18% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 114 | 33% helix, 27% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 69 | 71% helix, 0% strand | P0DTD1 |
| P | RNA (5'-R(P*AP*GP*AP*UP*UP*AP*AP*GP*UP*UP*AP*U)-3') | rna | 12 | — | — |
| T | RNA (5'-R(P*CP*CP*UP*AP*UP*AP*AP*CP*UP*UP*AP*AP*UP*CP*U)- 3') | rna | 15 | — | — |
| G | Non-structural protein 8 | protein | 106 | 24% helix, 25% strand | P0DTD1 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A
- HCU · [(2R)-4-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-(hydroxymethyl)butyl] dihydrogen phosphate · ligand · chains A, P, T
- MG · Magnesium ion · metal · 4 copies · chains A, P
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.81 | 0.97 | 28 | empty |
| 2 | 1174 | 0.80 | 0.82 | 84 | POP, MG, HCU |
| 3 | 500 | 0.69 | 0.79 | 61 | empty |
| 4 | 324 | 0.65 | 0.80 | 47 | MG, POP |
| 5 | 78 | 0.60 | 0.89 | 18 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2500 Ų buried · 17 hydrogen bonds · protein-protein
- C–G · 1220 Ų buried · 4 hydrogen bonds · protein-protein
- A–T · 1065 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–C · 878 Ų buried · 4 hydrogen bonds · protein-protein
- A–P · 624 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7DOI · Structure of COVID-19 RNA-dependent RNA polymerase bound to penciclovir. · 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 7DOI · PDBe 7DOI · UniProt P0DTD1
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