Research workbench
Zinc-free APOBEC3F catalytic domain crystal structure
Analyse Zinc-free APOBEC3F catalytic domain crystal structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HX4
- Type
- protein
- Length
- 345 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
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA dc->du-editing enzyme apobec-3F (EC 3.5.4.-) | protein | 177 | 44% helix, 25% strand | Q8IUX4 |
| B | DNA dc->du-editing enzyme apobec-3F (EC 3.5.4.-) | protein | 168 | 42% helix, 23% strand | Q8IUX4 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.68 | 0.78 | 58 | empty |
| 2 | 139 | 0.45 | 0.77 | 21 | empty |
| 3 | 77 | 0.39 | 0.78 | 23 | empty |
| 4 | 56 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 433 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5HX4 · Zinc-Free APOBEC3F Catalytic Domain Crystal Structure · 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 5HX4 · PDBe 5HX4 · UniProt Q8IUX4
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