Research workbench
SARS-coronavirus NSP12 bound to NSP7 and NSP8 co-factors
Analyse SARS-coronavirus NSP12 bound to NSP7 and NSP8 co-factors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NUR
- Type
- protein
- Length
- 1,087 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NSP12; NSP8; NSP7
- UniProt
- P0C6X7, P0C6U8
- Ligands
- ZN
- Pockets
- 16 · best druggability 0.67
Structure
electron microscopy · 4 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NSP12 | protein | 793 | 45% helix, 14% strand | P0C6X7 |
| B | NSP8 | protein | 115 | 41% helix, 26% strand | P0C6U8 |
| C | NSP7 | protein | 70 | 79% helix, 0% strand | P0C6X7 |
| D | NSP8 | protein | 109 | 31% helix, 28% strand | P0C6U8 |
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
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 379 | 0.67 | 0.81 | 44 | empty |
| 2 | 349 | 0.57 | 0.76 | 46 | empty |
| 3 | 50 | 0.57 | 0.91 | 26 | empty |
| 4 | 220 | 0.53 | 0.77 | 21 | empty |
| 5 | 72 | 0.48 | 0.83 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2497 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1338 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 730 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 165 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 144 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6NUR · SARS-Coronavirus NSP12 bound to NSP7 and NSP8 co-factors · 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 P0C6X7
- Every structure of UniProt P0C6U8
- Elsewhere: RCSB PDB 6NUR · PDBe 6NUR · UniProt P0C6X7 · UniProt P0C6U8
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