MolNFT v1 · #174426 · protein
Cryo-EM structure of the apo NSP12-NSP7-NSP8 complex
7BV1 · RNA-directed RNA polymerase: “Cryo-EM structure of the apo NSP12-NSP7-NSP8 complex”. Electron microscopy, 1 ligand (ZN), 15 pockets (best druggability 0.64). MolNFT v1 #174426 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7BV1
- Type
- protein
- Length
- 1,112 residues
- Chains
- 4
- 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
- ZN
- Pockets
- 15 · best druggability 0.64
Structure
electron microscopy · 4 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 836 | 43% helix, 15% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 114 | 39% helix, 26% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 63 | 76% helix, 0% strand | P0DTD1 |
| D | Non-structural protein 8 | protein | 99 | 25% helix, 20% strand | P0DTD1 |
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
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.64 | 0.79 | 42 | empty |
| 2 | 365 | 0.56 | 0.75 | 33 | empty |
| 3 | 164 | 0.56 | 0.81 | 32 | empty |
| 4 | 200 | 0.53 | 0.78 | 30 | empty |
| 5 | 62 | 0.53 | 0.87 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2361 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 975 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 799 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 157 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 144 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7BV1 · Cryo-EM structure of the apo nsp12-nsp7-nsp8 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 7BV1 · PDBe 7BV1 · UniProt P0DTD1
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