MolNFT v1 · #142163 · protein + DNA
APOBEC3F chimeric catalytic domain in complex with DNA(DT9)
5ZVB · APEBEC3F/SSDNA-T9: “APOBEC3F chimeric catalytic domain in complex with DNA(DT9)”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.62). MolNFT v1 #142163 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ZVB
- Type
- protein + DNA
- Length
- 374 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- APEBEC3F/SSDNA-T9; DNA (5'-D(*AP*TP*TP*TP*TP*CP*AP*AP*T)-3')
- EC
- 3.5.4.-
- UniProt
- Q9HC16, Q8IUX4
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | APEBEC3F/SSDNA-T9 (EC 3.5.4.-) | protein | 180 | 40% helix, 26% strand | Q9HC16, Q8IUX4 |
| B | APEBEC3F/SSDNA-T9 (EC 3.5.4.-) | protein | 185 | 39% helix, 25% strand | Q9HC16, Q8IUX4 |
| C | DNA (5'-D(*AP*TP*TP*TP*TP*CP*AP*AP*T)-3') | dna | 9 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CAC · Cacodylate ion · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.62 | 0.76 | 38 | empty |
| 2 | 69 | 0.35 | 0.76 | 20 | CAC |
Interfaces
3 interfaces between chains.
- B–C · 516 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–C · 426 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–B · 308 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 5ZVB · APOBEC3F Chimeric Catalytic Domain in Complex with DNA(dT9) · the same entry in another collection · chain C against C, 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 A against A, TM-score 0.97
- Q9HC16 · AlphaFold monomer V2.0 prediction for DNA dc->du-editing enzyme apobec-3G (Q9HC16) · a predicted model of the same protein · chain A against A, TM-score 0.93
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
- Every structure of UniProt Q8IUX4
- Elsewhere: RCSB PDB 5ZVB · PDBe 5ZVB · UniProt Q9HC16 · UniProt Q8IUX4
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