Research workbench
Crystal structure of the APOBEC3G catalytic domain
Analyse Crystal structure of the APOBEC3G catalytic domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IR2
- Type
- protein
- Length
- 375 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, MG, CL
- Pockets
- 5 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 38% 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 | 39% helix, 22% strand | Q9HC16 |
| B | DNA dc->du-editing enzyme apobec-3G (EC 3.5.4.-) | protein | 187 | 38% helix, 22% strand | Q9HC16 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.53 | 0.74 | 45 | empty |
| 2 | 122 | 0.42 | 0.76 | 18 | CL |
| 3 | 104 | 0.37 | 0.75 | 16 | CL |
| 4 | 80 | 0.37 | 0.77 | 16 | empty |
| 5 | 70 | 0.36 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 280 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
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 3IR2 · PDBe 3IR2 · UniProt Q9HC16
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