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Group deposition for crystallographic fragment screening of Chikungunya virus nsP3 macrodomain -- Crystal structure of Chikungunya virus nsP3 macrodomain in complex with Z385370362 (CHIKV_MacB-x0969)
Analyse Group deposition for crystallographic fragment screening of Chikungunya virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7H7T
- Type
- protein
- Length
- 648 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.34
- Source
- Chikungunya virus
- Molecule
- Non-structural protein 3
- EC
- 3.1.3.84
- UniProt
- Q8JUX6
- Ligands
- A1AQC, CL
- Pockets
- 9 · best druggability 0.64
Structure
x-ray diffraction · resolution 1.34 · 2 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Non-structural protein 3 (EC 3.1.3.84) | protein | 163 | 40% helix, 20% strand | Q8JUX6 |
| D | Non-structural protein 3 (EC 3.1.3.84) | protein | 159 | 40% helix, 21% strand | Q8JUX6 |
Ligands and binding sites
- A1AQC · (2,3-dihydro-1-benzofuran-5-yl)methanol · ligand · 6 copies · chains A, B, C, D
- CL · Chloride ion · ion · 9 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 18 copies · chains A, C, B, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.64 | 0.79 | 48 | DMS, CL, A1AQC |
| 2 | 336 | 0.62 | 0.78 | 38 | CL, DMS, A1AQC |
| 3 | 358 | 0.61 | 0.78 | 54 | DMS, CL, A1AQC |
| 4 | 211 | 0.61 | 0.81 | 28 | DMS, CL |
| 5 | 271 | 0.54 | 0.76 | 37 | empty |
Interfaces
4 interfaces between chains.
- C–D · 647 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 458 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 364 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 254 Ų buried · 3 hydrogen bonds · protein-protein
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 Q8JUX6
- Elsewhere: RCSB PDB 7H7T · PDBe 7H7T · UniProt Q8JUX6
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