MolNFT v1 · #184672 · protein + RNA
Dimeric form of SARS-cov-2 RNA-dependent RNA polymerase
7OYG · SARS-cov-2 RNA-dependent RNA polymerase (NSP12): “Dimeric form of SARS-cov-2 RNA-dependent RNA polymerase”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.80). MolNFT v1 #184672 on GenesisL1: 3D structure…
- PDB
- 7OYG
- Type
- protein + RNA
- Length
- 1,958 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SARS-cov-2 RNA-dependent RNA polymerase (NSP12); SARS-cov-2 NSP8; SARS-cov-2 NSP7; RNA…
- EC
- 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-
- UniProt
- P0DTD1
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 5 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | SARS-cov-2 RNA-dependent RNA polymerase (NSP12) (EC 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-) | protein | 814 | 46% helix, 16% strand | P0DTD1 |
| B, E | SARS-cov-2 NSP8 (EC 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-) | protein | 81 | 21% helix, 36% strand | P0DTD1 |
| C, F | SARS-cov-2 NSP7 (EC 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-) | protein | 62 | 87% helix, 0% strand | P0DTD1 |
| P, G | RNA (5'-R(P*CP*UP*AP*CP*GP*CP*AP*GP*UP*G)-3') | rna | 10 | — | — |
| T, H | RNA (5'-R(P*UP*GP*CP*AP*CP*UP*GP*CP*GP*UP*AP*G)-3') | rna | 12 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.80 | 0.97 | 27 | empty |
| 2 | 951 | 0.80 | 0.82 | 81 | empty |
| 3 | 1057 | 0.80 | 0.82 | 78 | empty |
| 4 | 137 | 0.79 | 0.97 | 27 | empty |
| 5 | 505 | 0.70 | 0.80 | 70 | empty |
Interfaces
13 interfaces between chains.
- D–E · 1444 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1435 Ų buried · 9 hydrogen bonds · protein-protein
- D–H · 1096 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–T · 1092 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–C · 820 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7OYG · Dimeric form of SARS-CoV-2 RNA-dependent RNA polymerase · 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 7OYG · PDBe 7OYG · UniProt P0DTD1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.