Research workbench
APOBEC3F catalytic domain complex with a single-stranded DNA
Analyse APOBEC3F catalytic domain complex with a single-stranded DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W2M
- Type
- protein + DNA
- Length
- 1,492 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA dc->du-editing enzyme apobec-3F; DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
- EC
- 3.5.4.-
- UniProt
- Q8IUX4
- Ligands
- ZN
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, J, K, L, M | DNA dc->du-editing enzyme apobec-3F (EC 3.5.4.-) | protein | 184 | 35% helix, 20% strand | Q8IUX4 |
| E, N | DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') | dna | 10 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, C, B, D, J, L, K, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 761 | 0.81 | 0.84 | 69 | empty |
| 2 | 818 | 0.80 | 0.83 | 73 | empty |
| 3 | 511 | 0.80 | 0.86 | 54 | empty |
| 4 | 486 | 0.79 | 0.86 | 52 | empty |
| 5 | 594 | 0.65 | 0.75 | 31 | empty |
Interfaces
23 interfaces between chains.
- A–C · 473 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 473 Ų buried · 4 hydrogen bonds · protein-protein
- K–M · 466 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 465 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–E · 465 Ų buried · 3 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5W2M · APOBEC3F Catalytic Domain Complex with a Single-Stranded DNA · the same entry in another collection · chain N against N, TM-score 1.00
- Q8IUX4 · AlphaFold monomer V2.0 prediction for DNA dc->du-editing enzyme apobec-3F (Q8IUX4) · a predicted model of the same protein · chain B 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 Q8IUX4
- Elsewhere: RCSB PDB 5W2M · PDBe 5W2M · UniProt Q8IUX4
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