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
- 6W8Y
- 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
- TJJ
- Pockets
- 8 · best druggability 0.67
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 | 37% helix, 20% strand | A0A4D6GPC4 |
Ligands and binding sites
- TJJ · 2-oxo-2,3-dihydropyrimidine-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
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.67 | 0.78 | 54 | TJJ |
| 2 | 402 | 0.66 | 0.79 | 44 | TJJ |
| 3 | 232 | 0.62 | 0.81 | 31 | TJJ |
| 4 | 199 | 0.61 | 0.82 | 29 | TJJ |
| 5 | 314 | 0.58 | 0.77 | 40 | empty |
Interfaces
4 interfaces between chains.
- B–C · 593 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 443 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 438 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 246 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6W8Y · 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 6W8Y · PDBe 6W8Y · UniProt A0A4D6GPC4
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