Research workbench
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 v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 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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