MolNFT v1 · #158051 · protein
Cryoem structure of the truncated HIV-1 VIF/CBFBETA/A3F complex
6NIL · DNA dc->du-editing enzyme apobec-3F: “Cryoem structure of the truncated HIV-1 VIF/CBFBETA/A3F complex”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.76). MolNFT v1 #158051 on GenesisL1: 3D structure, binding…
- PDB
- 6NIL
- Type
- protein
- Length
- 1,800 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA dc->du-editing enzyme apobec-3F; Core-binding factor subunit beta; Virion infectivity…
- EC
- 3.5.4.38
- UniProt
- Q8IUX4, Q13951, P12504, A0A346ARH7
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 3 distinct chains · 27% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | DNA dc->du-editing enzyme apobec-3F (EC 3.5.4.38) | protein | 177 | 37% helix, 16% strand | Q8IUX4 |
| B, E, H, K | Core-binding factor subunit beta | protein | 140 | 22% helix, 34% strand | Q13951 |
| C, F, I, L | Virion infectivity factor | protein | 133 | 18% helix, 28% strand | P12504, A0A346ARH7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, D, G, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.76 | 0.78 | 94 | empty |
| 2 | 902 | 0.75 | 0.78 | 80 | empty |
| 3 | 809 | 0.73 | 0.78 | 74 | empty |
| 4 | 675 | 0.73 | 0.79 | 60 | empty |
| 5 | 278 | 0.64 | 0.81 | 39 | empty |
Interfaces
28 interfaces between chains.
- E–F · 2240 Ų buried · 36 hydrogen bonds · protein-protein
- K–L · 2240 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 2234 Ų buried · 36 hydrogen bonds · protein-protein
- H–I · 2234 Ų buried · 36 hydrogen bonds · protein-protein
- D–F · 726 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6NIL · cryoEM structure of the truncated HIV-1 Vif/CBFbeta/A3F complex · the same entry in another collection · chain L against L, 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 Q8IUX4
- Every structure of UniProt Q13951
- Every structure of UniProt P12504
- Every structure of UniProt A0A346ARH7
- Elsewhere: RCSB PDB 6NIL · PDBe 6NIL · UniProt Q8IUX4 · UniProt Q13951 · UniProt P12504 · UniProt A0A346ARH7
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