Research workbench
The thermo- and acido-stable orf-99 from the archaeal virus AFV1
Analyse The thermo- and acido-stable orf-99 from the archaeal virus AFV1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DF6
- Type
- protein
- Length
- 394 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ORF99
- UniProt
- Q70LE8
- Ligands
- CA
- Pockets
- 2 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | ORF99 | protein | 98 | 24% helix, 54% strand | Q70LE8 |
| B, C | ORF99 | protein | 99 | 25% helix, 55% strand | Q70LE8 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.83 | 0.90 | 37 | empty |
| 2 | 72 | 0.30 | 0.73 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 879 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 850 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 443 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3DF6 · The thermo- and acido-stable ORF-99 from the archaeal virus AFV1 · 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 Q70LE8
- Elsewhere: RCSB PDB 3DF6 · PDBe 3DF6 · UniProt Q70LE8
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