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
- 6W0T
- Type
- protein
- Length
- 639 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 3
- EC
- 3.1.3.84
- UniProt
- Q5XXP4
- Ligands
- S6Y
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Non-structural protein 3 (EC 3.1.3.84) | protein | 160 | 38% helix, 20% strand | Q5XXP4 |
| D | Non-structural protein 3 (EC 3.1.3.84) | protein | 159 | 38% helix, 19% strand | Q5XXP4 |
Ligands and binding sites
- S6Y · 6-(2-methylpropyl)-2-oxidanylidene-5~{H}-pyrimidine-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 | 422 | 0.68 | 0.80 | 55 | S6Y |
| 2 | 436 | 0.65 | 0.78 | 59 | empty |
| 3 | 226 | 0.61 | 0.81 | 30 | S6Y |
| 4 | 268 | 0.61 | 0.79 | 37 | S6Y |
| 5 | 187 | 0.58 | 0.81 | 29 | S6Y |
Interfaces
4 interfaces between chains.
- C–D · 601 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 442 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 373 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 258 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6W0T · 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 Q5XXP4
- Elsewhere: RCSB PDB 6W0T · PDBe 6W0T · UniProt Q5XXP4
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