MolNFT v1 · #176491 · protein + RNA
Structure of COVID-19 RNA-dependent RNA polymerase (extended conformation) bound to penciclovir
7DOK · RNA (5'- R(P*GP*CP*UP*AP*UP*GP*UP*GP*AP*GP*AP*UP*UP*AP*AP*GP…: “Structure of COVID-19 RNA-dependent RNA polymerase (extended conformation) bound to penciclovir”. Electron microscopy, 4 ligands (POP, HCU, MG), 12 pockets (best…
- PDB
- 7DOK
- Type
- protein + RNA
- Length
- 1,367 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'- R(P*GP*CP*UP*AP*UP*GP*UP*GP*AP*GP*AP*UP*UP*AP*AP*GP*UP*UP*AP*U)-3'); RNA (5'…
- EC
- 2.7.7.48
- UniProt
- P0DTD1
- Ligands
- POP, HCU, MG, ZN
- Pockets
- 12 · best druggability 0.80
Structure
electron microscopy · 6 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | RNA (5'- R(P*GP*CP*UP*AP*UP*GP*UP*GP*AP*GP*AP*UP*UP*AP*AP*GP*UP*UP*AP*U)-3') | rna | 20 | — | — |
| T | RNA (5'- R(P*CP*CP*CP*UP*AP*UP*AP*AP*CP*UP*UP*AP*AP*UP*CP*UP*CP*AP*CP*AP*UP*AP *GP*C)-3') | rna | 24 | — | — |
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 925 | 41% helix, 18% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 155 | 54% helix, 18% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 69 | 71% helix, 0% strand | P0DTD1 |
| G | Non-structural protein 8 | protein | 174 | 52% helix, 16% 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 P, T, A
- MG · Magnesium ion · metal · 4 copies · chains P, A
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.80 | 0.97 | 28 | empty |
| 2 | 1091 | 0.79 | 0.81 | 73 | HCU, MG, POP |
| 3 | 565 | 0.71 | 0.80 | 34 | empty |
| 4 | 520 | 0.69 | 0.79 | 66 | empty |
| 5 | 298 | 0.65 | 0.81 | 46 | MG, POP |
Interfaces
12 interfaces between chains.
- A–B · 2523 Ų buried · 15 hydrogen bonds · protein-protein
- C–G · 1286 Ų buried · 5 hydrogen bonds · protein-protein
- T–A · 1105 Ų buried · 19 hydrogen bonds · protein-nucleic
- P–T · 921 Ų buried · 77 hydrogen bonds · nucleic-nucleic
- A–C · 846 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7DOK · Structure of COVID-19 RNA-dependent RNA polymerase (extended conformation) bound to… · the same entry in another collection · chain P against P, 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 7DOK · PDBe 7DOK · UniProt P0DTD1
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