Research workbench
Crystal structure of a primate APOBEC3G N-terminal domain
Analyse Crystal structure of a primate APOBEC3G N-terminal domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K82
- Type
- protein
- Length
- 755 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apolipoprotein B mRNA editing enzyme, catalytic peptide- like 3G,APOLIPOPROTEIN B mRNA…
- UniProt
- M1GSK9
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Apolipoprotein B mRNA editing enzyme, catalytic peptide- like 3G,APOLIPOPROTEIN B mRNA editing enzyme, catalytic peptide-like 3G | protein | 188 | 42% helix, 18% strand | M1GSK9 |
| D | Apolipoprotein B mRNA editing enzyme, catalytic peptide- like 3G,APOLIPOPROTEIN B mRNA editing enzyme, catalytic peptide-like 3G | protein | 191 | 40% helix, 17% strand | M1GSK9 |
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
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.46 | 0.82 | 17 | empty |
| 2 | 60 | 0.37 | 0.79 | 17 | empty |
| 3 | 108 | 0.37 | 0.74 | 22 | empty |
| 4 | 50 | 0.36 | 0.80 | 18 | empty |
| 5 | 77 | 0.36 | 0.76 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–C · 753 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 734 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 653 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5K82 · Crystal Structure of a Primate APOBEC3G N-Terminal Domain · the same entry in another collection · chain A against A, TM-score 1.00
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 M1GSK9
- Elsewhere: RCSB PDB 5K82 · PDBe 5K82 · UniProt M1GSK9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.