Research workbench
First-in-class small molecule inhibitors of the single-strand DNA cytosine deaminase APOBEC3G
Analyse First-in-class small molecule inhibitors of the single-strand DNA cytosine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V4J
- Type
- protein
- Length
- 369 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA dc->du-editing enzyme apobec-3G
- EC
- 3.5.4.-
- UniProt
- Q9HC16
- Ligands
- PQR, ZN
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA dc->du-editing enzyme apobec-3G (EC 3.5.4.-) | protein | 184 | 39% helix, 23% strand | Q9HC16 |
| B | DNA dc->du-editing enzyme apobec-3G (EC 3.5.4.-) | protein | 185 | 37% helix, 23% strand | Q9HC16 |
Ligands and binding sites
- PQR · 4-[methyl(nitroso)amino]benzene-1,2-diol · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 662 | 0.68 | 0.77 | 67 | PQR |
| 2 | 57 | 0.35 | 0.78 | 13 | empty |
| 3 | 53 | 0.34 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 429 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3V4J · First-In-Class Small Molecule Inhibitors of the Single-strand DNA Cytosine Deaminase… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HC16 · AlphaFold monomer V2.0 prediction for DNA dc->du-editing enzyme apobec-3G (Q9HC16) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9HC16
- Elsewhere: RCSB PDB 3V4J · PDBe 3V4J · UniProt Q9HC16
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