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Crystal structure of the HIV-1 vif binding, catalytically active domain of APOBEC3F
Analyse Crystal structure of the HIV-1 vif binding, catalytically active domain of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IOU
- Type
- protein
- Length
- 713 residues
- Chains
- 4
- 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
- 6 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA dc->du-editing enzyme apobec-3F (EC 3.5.4.-) | protein | 178 | 39% helix, 21% strand | Q8IUX4 |
| B, D | DNA dc->du-editing enzyme apobec-3F (EC 3.5.4.-) | protein | 179 | 39% helix, 24% strand | Q8IUX4 |
| C | DNA dc->du-editing enzyme apobec-3F (EC 3.5.4.-) | protein | 177 | 38% helix, 23% strand | Q8IUX4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.51 | 0.81 | 26 | empty |
| 2 | 129 | 0.42 | 0.76 | 19 | empty |
| 3 | 125 | 0.42 | 0.76 | 20 | empty |
| 4 | 81 | 0.37 | 0.77 | 21 | empty |
| 5 | 90 | 0.34 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–D · 678 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 639 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 607 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4IOU · Crystal structure of the HIV-1 Vif binding, catalytically active domain of APOBEC3F · the same entry in another collection · chain D against D, 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 0.97
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 4IOU · PDBe 4IOU · UniProt Q8IUX4
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