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Delicate structural coordination of the Severe Acute Respiratory Syndrome coronavirus Nsp13 upon ATP hydrolysis
Analyse Delicate structural coordination of the Severe Acute Respiratory Syndrome… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JYT
- Type
- protein
- Length
- 1,194 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Human SARS coronavirus
- Molecule
- Helicase
- EC
- 3.6.4.12, 3.6.4.13
- UniProt
- P0C6X7
- Ligands
- ZN
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.8 · 2 distinct chains · 20% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Helicase (EC 3.6.4.12, 3.6.4.13) | protein | 597 | 20% helix, 17% strand | P0C6X7 |
| B | Helicase (EC 3.6.4.12, 3.6.4.13) | protein | 597 | 19% helix, 19% strand | P0C6X7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.81 | 0.82 | 134 | empty |
| 2 | 806 | 0.81 | 0.84 | 79 | empty |
| 3 | 907 | 0.79 | 0.82 | 84 | empty |
| 4 | 437 | 0.74 | 0.83 | 48 | empty |
| 5 | 566 | 0.69 | 0.78 | 53 | empty |
Interfaces
1 interface between chains.
- A–B · 1338 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 6JYT · Delicate structural coordination of the severe acute respiratory syndrome coronavirus… · 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
- Elsewhere: RCSB PDB 6JYT · PDBe 6JYT · UniProt P0C6X7
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