MolNFT v1 · #106092 · protein
The crystal structure of novel APOBEC3G CD2 head-to-tail dimer suggests the binding mode of full-length APOBEC3G to HIV-1 ssdna
4ROV · DNA dc->du-editing enzyme apobec-3G: “The crystal structure of novel APOBEC3G CD2 head-to-tail dimer suggests the binding mode of full-length…”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.67). MolNFT v1 #106092…
- PDB
- 4ROV
- Type
- protein
- Length
- 360 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
- ZN
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA dc->du-editing enzyme apobec-3G (EC 3.5.4.-) | protein | 188 | 40% helix, 21% strand | Q9HC16 |
| B | DNA dc->du-editing enzyme apobec-3G (EC 3.5.4.-) | protein | 172 | 42% helix, 22% strand | Q9HC16 |
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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.67 | 0.84 | 32 | empty |
| 2 | 119 | 0.39 | 0.75 | 19 | empty |
| 3 | 69 | 0.38 | 0.78 | 14 | empty |
| 4 | 65 | 0.36 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 558 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4ROV · The crystal structure of novel APOBEC3G CD2 head-to-tail dimer suggests the binding mode… · 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 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 Q9HC16
- Elsewhere: RCSB PDB 4ROV · PDBe 4ROV · UniProt Q9HC16
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