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The 1.5 a crystal structure of the co-factor complex of NSP7 and the C-terminal domain of NSP8 from SARS cov-2
Analyse The 1.5 a crystal structure of the co-factor complex of NSP7 and the C-terminal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XIP
- Type
- protein
- Length
- 379 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
- 4 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-structural protein 7 | protein | 72 | 76% helix, 0% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 115 | 38% helix, 26% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 75 | 73% helix, 0% strand | P0DTD1 |
| D | Non-structural protein 8 | protein | 117 | 38% helix, 26% strand | P0DTD1 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 528 | 0.66 | 0.78 | 45 | EDO |
| 2 | 55 | 0.38 | 0.80 | 14 | empty |
| 3 | 58 | 0.36 | 0.79 | 15 | empty |
| 4 | 54 | 0.28 | 0.74 | 13 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1457 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1417 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 199 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 196 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 108 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6XIP · The 1.5 A Crystal Structure of the Co-factor Complex of NSP7 and the C-terminal Domain of… · 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 6XIP · PDBe 6XIP · UniProt P0DTD1
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