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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 Z1741982125 (CHIKV_MacB-x1118)
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
- 7H83
- Type
- protein
- Length
- 648 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.45
- Source
- Chikungunya virus
- Molecule
- Non-structural protein 3
- EC
- 3.1.3.84
- UniProt
- Q8JUX6
- Ligands
- T5Y, CL
- Pockets
- 9 · best druggability 0.65
Structure
x-ray diffraction · resolution 1.45 · 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, 20% strand | Q8JUX6 |
Ligands and binding sites
- T5Y · pyridin-2-ol · ligand · 10 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 9 copies · chains A, C, B, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.65 | 0.82 | 36 | DMS, CL, T5Y |
| 2 | 194 | 0.65 | 0.84 | 28 | DMS, CL, T5Y |
| 3 | 314 | 0.61 | 0.79 | 47 | empty |
| 4 | 251 | 0.60 | 0.80 | 44 | CL, DMS, T5Y |
| 5 | 199 | 0.59 | 0.81 | 28 | DMS, CL, T5Y |
Interfaces
4 interfaces between chains.
- C–D · 641 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 477 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 342 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 220 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 7H83 · PDBe 7H83 · UniProt Q8JUX6
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