MolNFT v1 · #167768 · protein
Crystal structure of chikv NSP3 macrodomain soaked with ADP-ribose
6VUQ · Nonstructural polyprotein: “Crystal structure of chikv NSP3 macrodomain soaked with ADP-ribose”. X-ray diffraction, 1 ligand (APR), 8 pockets (best druggability 0.65). MolNFT v1 #167768 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6VUQ
- Type
- protein
- Length
- 639 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nonstructural polyprotein
- UniProt
- A0A4D6GPC4
- Ligands
- APR
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nonstructural polyprotein | protein | 161 | 39% helix, 19% strand | A0A4D6GPC4 |
| B | Nonstructural polyprotein | protein | 159 | 40% helix, 19% strand | A0A4D6GPC4 |
| C | Nonstructural polyprotein | protein | 160 | 39% helix, 19% strand | A0A4D6GPC4 |
| D | Nonstructural polyprotein | protein | 159 | 40% helix, 19% strand | A0A4D6GPC4 |
Ligands and binding sites
- APR · Adenosine-5-diphosphoribose · 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 | 0.65 | 0.78 | 54 | APR |
| 2 | 363 | 0.63 | 0.79 | 46 | APR |
| 3 | 341 | 0.62 | 0.78 | 42 | empty |
| 4 | 206 | 0.61 | 0.82 | 30 | APR |
| 5 | 235 | 0.61 | 0.80 | 30 | APR |
Interfaces
5 interfaces between chains.
- B–D · 592 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 442 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 368 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 206 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 22 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6VUQ · Crystal structure of CHIKV nsP3 macrodomain soaked with ADP-ribose · 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 6VUQ · PDBe 6VUQ · UniProt A0A4D6GPC4
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