MolNFT v1 · #115664 · protein
Crystal structure of the cancer genomic DNA mutator APOBEC3B
5CQD · DNA dc->du-editing enzyme apobec-3B: “Crystal structure of the cancer genomic DNA mutator APOBEC3B”. X-ray diffraction, 1 ligand (ZN), 1 pocket (best druggability 0.73). MolNFT v1 #115664 on GenesisL1: 3D structure, binding sites…
- PDB
- 5CQD
- 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-3B
- EC
- 3.5.4.-
- UniProt
- Q9UH17
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA dc->du-editing enzyme apobec-3B (EC 3.5.4.-) | protein | 185 | 36% helix, 24% strand | Q9UH17 |
| C | DNA dc->du-editing enzyme apobec-3B (EC 3.5.4.-) | protein | 184 | 36% helix, 27% strand | Q9UH17 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.73 | 0.82 | 51 | empty |
Interfaces
1 interface between chains.
- A–C · 368 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5CQD · Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UH17 · AlphaFold monomer V2.0 prediction for DNA dc->du-editing enzyme apobec-3B (Q9UH17) · a predicted model of the same protein · chain C 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 Q9UH17
- Elsewhere: RCSB PDB 5CQD · PDBe 5CQD · UniProt Q9UH17
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