Research workbench
Group deposition of Chikungunya virus nsP3 macrodomain in complex with inhibitors from the READDI-AC AViDD center -- Crystal structure of Chikungunya virus nsP3 macrodomain in complex with RA-0188465-01 (CHIKV_MacB-x2188)
Analyse Group deposition of Chikungunya virus nsP3 macrodomain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7HIM
- Type
- protein
- Length
- 648 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.74
- Source
- Chikungunya virus
- Molecule
- Non-structural protein 3
- EC
- 3.1.3.84
- UniProt
- Q8JUX6
- Ligands
- A1BCG, CL
- Pockets
- 9 · best druggability 0.63
Structure
x-ray diffraction · resolution 1.74 · 2 distinct chains · 41% 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 | 42% helix, 21% strand | Q8JUX6 |
Ligands and binding sites
- A1BCG · 2-(2-oxopyridin-1(2H)-yl)ethyl 3-methyl-1H-pyrrolo[2,3-b]pyridine-5-carboxylate · ligand · chains A
- CL · Chloride ion · ion · 10 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 19 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.63 | 0.80 | 51 | DMS, CL |
| 2 | 348 | 0.63 | 0.79 | 46 | DMS, CL |
| 3 | 205 | 0.60 | 0.81 | 29 | DMS, CL |
| 4 | 197 | 0.59 | 0.81 | 28 | DMS, CL |
| 5 | 132 | 0.53 | 0.81 | 18 | empty |
Interfaces
4 interfaces between chains.
- C–D · 623 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 454 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 380 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 263 Ų buried · 2 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 7HIM · PDBe 7HIM · UniProt Q8JUX6
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