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Crystal structure of ORF140 of the archaeal virus acidianus filamentous virus 1 (AFV1)
Analyse Crystal structure of ORF140 of the archaeal virus acidianus filamentous virus 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FBZ
- Type
- protein
- Length
- 492 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein
- UniProt
- Q70LC6
- Ligands
- CL
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 80% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative uncharacterized protein | protein | 123 | 84% helix, 2% strand | Q70LC6 |
| C | Putative uncharacterized protein | protein | 124 | 78% helix, 2% strand | Q70LC6 |
| D | Putative uncharacterized protein | protein | 122 | 80% helix, 2% strand | Q70LC6 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains B, D
- BOG · octyl beta-D-glucopyranoside · additive · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.81 | 0.83 | 81 | BOG |
| 2 | 534 | 0.77 | 0.84 | 58 | BOG |
| 3 | 188 | 0.61 | 0.82 | 27 | BOG |
| 4 | 58 | 0.33 | 0.77 | 12 | empty |
| 5 | 54 | 0.29 | 0.75 | 9 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1595 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1585 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1406 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1399 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 443 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3FBZ · Crystal structure of ORF140 of the archaeal virus Acidianus Filamentous Virus 1 (AFV1) · the same entry in another collection · chain C against C, 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 Q70LC6
- Elsewhere: RCSB PDB 3FBZ · PDBe 3FBZ · UniProt Q70LC6
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