MolNFT v1 · #168166 · protein
Co-crystal structures of chikv NSP3 macrodomain with pyrimidone fragments
6W7H · Nonstructural polyprotein: “Co-crystal structures of chikv NSP3 macrodomain with pyrimidone fragments”. X-ray diffraction, 1 ligand (TEV), 8 pockets (best druggability 0.66). MolNFT v1 #168166 on GenesisL1: 3D structure, binding…
- PDB
- 6W7H
- Type
- protein
- Length
- 640 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nonstructural polyprotein
- UniProt
- A0A4D6GPC4
- Ligands
- TEV
- Pockets
- 8 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Nonstructural polyprotein | protein | 160 | 38% helix, 20% strand | A0A4D6GPC4 |
Ligands and binding sites
- TEV · 6-methyl-2-oxo-2,5-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 | 489 | 0.66 | 0.78 | 57 | TEV |
| 2 | 341 | 0.65 | 0.80 | 45 | TEV |
| 3 | 442 | 0.62 | 0.77 | 57 | empty |
| 4 | 199 | 0.60 | 0.82 | 32 | TEV |
| 5 | 192 | 0.58 | 0.81 | 28 | TEV |
Interfaces
4 interfaces between chains.
- B–C · 588 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 436 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 340 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 234 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6W7H · 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 6W7H · PDBe 6W7H · UniProt A0A4D6GPC4
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