Research workbench
Crystal structure of human APOBEC3B variant complexed with ssdna
Analyse Crystal structure of human APOBEC3B variant complexed with ssdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TD5
- Type
- protein + DNA
- Length
- 183 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA dc->du-editing enzyme apobec-3B; DNA (5'-D(P*TP*TP*CP*AP*T)-3')
- EC
- 3.5.4.-
- UniProt
- Q9UH17
- Ligands
- ZN, IOD, CL
- Pockets
- 1 · best druggability 0.29
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA dc->du-editing enzyme apobec-3B (EC 3.5.4.-) | protein | 179 | 40% helix, 21% strand | Q9UH17 |
| C | DNA (5'-D(P*TP*TP*CP*AP*T)-3') | dna | 4 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- IOD · Iodide ion · ion · 9 copies · chains A, C
- CL · Chloride ion · ion · 2 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.29 | 0.76 | 15 | IOD, EDO |
Interfaces
1 interface between chains.
- A–C · 639 Ų buried · 16 hydrogen bonds · protein-nucleic
Compared structures
- 5TD5 · Crystal Structure of Human APOBEC3B variant complexed with ssDNA · 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 A against A, TM-score 0.97
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 5TD5 · PDBe 5TD5 · UniProt Q9UH17
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