Research workbench
Crystal structure of the vif-binding domain of human APOBEC3F
Analyse Crystal structure of the vif-binding domain of human APOBEC3F in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WUS
- Type
- protein
- Length
- 368 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA dc->du-editing enzyme apobec-3F
- EC
- 3.5.4.-
- UniProt
- Q8IUX4
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.43
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA dc->du-editing enzyme apobec-3F (EC 3.5.4.-) | protein | 184 | 38% helix, 24% strand | Q8IUX4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.43 | 0.80 | 17 | empty |
| 2 | 121 | 0.40 | 0.75 | 23 | empty |
| 3 | 111 | 0.38 | 0.74 | 15 | empty |
| 4 | 52 | 0.37 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 318 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3WUS · Crystal Structure of the Vif-Binding Domain of Human APOBEC3F · the same entry in another collection · chain A against A, TM-score 1.00
- Q8IUX4 · AlphaFold monomer V2.0 prediction for DNA dc->du-editing enzyme apobec-3F (Q8IUX4) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q8IUX4
- Elsewhere: RCSB PDB 3WUS · PDBe 3WUS · UniProt Q8IUX4
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