Research workbench
Co-crystal structures of chikv NSP3 macrodomain with pyrimidone fragments
Analyse Co-crystal structures of chikv NSP3 macrodomain with pyrimidone fragments in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W8Q
- Type
- protein
- Length
- 642 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nonstructural polyprotein
- UniProt
- A0A4D6GPC4
- Ligands
- TJS
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Nonstructural polyprotein | protein | 160 | 38% helix, 20% strand | A0A4D6GPC4 |
| D | Nonstructural polyprotein | protein | 162 | 38% helix, 20% strand | A0A4D6GPC4 |
Ligands and binding sites
- TJS · 2-oxo-1,2,5,6,7,8-hexahydroquinazoline-4-carboxylic acid · ligand · 4 copies · chains A, B, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 561 | 0.69 | 0.78 | 58 | TJS |
| 2 | 441 | 0.66 | 0.78 | 49 | TJS |
| 3 | 258 | 0.62 | 0.80 | 32 | TJS |
| 4 | 213 | 0.58 | 0.80 | 30 | TJS |
| 5 | 289 | 0.57 | 0.77 | 44 | empty |
Interfaces
5 interfaces between chains.
- B–C · 589 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 449 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 418 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 246 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6W8Q · Co-crystal structures of CHIKV nsP3 macrodomain with pyrimidone fragments · 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 A0A4D6GPC4
- Elsewhere: RCSB PDB 6W8Q · PDBe 6W8Q · UniProt A0A4D6GPC4
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