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Crystal structure of macro domain of chikungunya virus in complex with ADP-ribose
Analyse Crystal structure of macro domain of chikungunya virus in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GPO
- Type
- protein
- Length
- 640 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 3
- UniProt
- Q8JUX6
- Ligands
- APR
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-structural protein 3 | protein | 162 | 38% helix, 19% strand | Q8JUX6 |
| B, C | Non-structural protein 3 | protein | 160 | 40% helix, 19% strand | Q8JUX6 |
| D | Non-structural protein 3 | protein | 158 | 39% helix, 20% strand | Q8JUX6 |
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
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.66 | 0.76 | 71 | empty |
| 2 | 205 | 0.62 | 0.82 | 29 | APR |
| 3 | 319 | 0.60 | 0.78 | 39 | APR |
| 4 | 232 | 0.60 | 0.80 | 32 | APR |
| 5 | 220 | 0.59 | 0.80 | 29 | APR |
Interfaces
4 interfaces between chains.
- B–C · 449 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 285 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 246 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 68 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3GPO · Crystal structure of macro domain of Chikungunya virus in complex 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 Q8JUX6
- Elsewhere: RCSB PDB 3GPO · PDBe 3GPO · UniProt Q8JUX6
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