MolNFT v1 · #188222 · protein
SARS-cov-2 NSP12/7/8 complex with a native N-terminus NSP9
7THM · RNA-directed RNA polymerase: “SARS-cov-2 NSP12/7/8 complex with a native N-terminus NSP9”. Electron microscopy, 3 ligands (POP, ZN, MN), 18 pockets (best druggability 0.66). MolNFT v1 #188222 on GenesisL1: 3D structure, binding…
- PDB
- 7THM
- Type
- protein
- Length
- 1,150 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase; Non-structural protein 8; Non-structural protein 7…
- EC
- 2.7.7.48
- UniProt
- P0DTD1
- Ligands
- POP, ZN, MN
- Pockets
- 18 · best druggability 0.66
Structure
electron microscopy · 5 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 860 | 42% helix, 14% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 108 | 33% helix, 23% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 37 | 70% helix, 0% strand | P0DTD1 |
| D | Non-structural protein 8 | protein | 71 | 32% helix, 25% strand | P0DTD1 |
| G | Non-structural protein 9 | protein | 74 | 11% helix, 22% strand | P0DTD1 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · chains A, G
- ZN · Zinc ion · metal · 2 copies · chains A
- MN · Manganese (II) ion · metal · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.66 | 0.79 | 49 | empty |
| 2 | 459 | 0.64 | 0.77 | 54 | empty |
| 3 | 127 | 0.59 | 0.85 | 28 | empty |
| 4 | 153 | 0.58 | 0.83 | 30 | empty |
| 5 | 200 | 0.57 | 0.80 | 38 | MN, POP |
Interfaces
6 interfaces between chains.
- A–B · 2265 Ų buried · 15 hydrogen bonds · protein-protein
- A–G · 844 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 764 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 507 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 100 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7THM · SARS-CoV-2 nsp12/7/8 complex with a native N-terminus nsp9 · 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 7THM · PDBe 7THM · UniProt P0DTD1
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