MolNFT v1 · #168761 · protein
The 1.95 a crystal structure of the co-factor complex of NSP7 and the C-terminal domain of NSP8 from SARS-cov-2
6WQD · Non-structural protein 7: “The 1.95 a crystal structure of the co-factor complex of NSP7 and the C-terminal domain of NSP8 from…”. X-ray diffraction, 1 pocket (best druggability 0.58). MolNFT v1 #168761 on GenesisL1: 3D structure…
- PDB
- 6WQD
- Type
- protein
- Length
- 382 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 7; Non-structural protein 8
- UniProt
- P0DTD1
- Pockets
- 1 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-structural protein 7 | protein | 74 | 74% helix, 3% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 121 | 36% helix, 25% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 73 | 74% helix, 0% strand | P0DTD1 |
| D | Non-structural protein 8 | protein | 114 | 38% helix, 26% strand | P0DTD1 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.58 | 0.78 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1408 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1400 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 465 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 438 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 227 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6WQD · The 1.95 A Crystal Structure of the Co-factor Complex of NSP7 and the C-terminal Domain… · 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 6WQD · PDBe 6WQD · UniProt P0DTD1
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