MolNFT v2 · #211478 · protein + RNA
Cryo-EM structure of APOBEC3G-Vif complex
8H0I: “Cryo-EM structure of APOBEC3G-Vif complex”. Electron microscopy at 2.8, 2 ligands (ZN, CL), 20 pockets (best druggability 0.85). MolNFT v2 #211478 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 8H0I
- Type
- protein + RNA
- Length
- 1,748 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Homo sapiens; Human immunodeficiency virus 1; SYNTHETIC CONSTRUCT
- Molecule
- APOBEC3G; Viral infectivity factor; Core binding factor beta; RNA…
- UniProt
- Q13951
- Ligands
- ZN, CL
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · resolution 2.8 · 6 distinct chains · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | APOBEC3G | protein | 345 | 40% helix, 25% strand | — |
| C, G | Viral infectivity factor | protein | 129 | 26% helix, 29% strand | — |
| D, H | Core binding factor beta | protein | 129 | 33% helix, 35% strand | Q13951 |
| E, I | Viral infectivity factor | protein | 128 | 27% helix, 34% strand | — |
| F, J | Core binding factor beta | protein | 124 | 27% helix, 37% strand | Q13951 |
| X, Y | RNA (5'-R(*CP*GP*GP*UP*UP*GP*AP*UP*CP*GP*UP*UP*UP*UP*AP*AP*CP*AP*A)-3') | rna | 19 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 849 | 0.85 | 0.87 | 83 | empty |
| 2 | 674 | 0.83 | 0.87 | 80 | empty |
| 3 | 997 | 0.82 | 0.83 | 81 | empty |
| 4 | 1171 | 0.80 | 0.82 | 71 | empty |
| 5 | 934 | 0.79 | 0.81 | 83 | empty |
Interfaces
31 interfaces between chains.
- G–H · 2319 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2314 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 2121 Ų buried · 29 hydrogen bonds · protein-protein
- I–J · 2113 Ų buried · 27 hydrogen bonds · protein-protein
- B–Y · 1449 Ų buried · 30 hydrogen bonds · protein-nucleic
Compared structures
- Q13951 · AlphaFold monomer V2.0 prediction for core-binding factor subunit beta (Q13951) · a predicted model of the same protein · chain D against A, TM-score 0.69
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 Q13951
- Elsewhere: RCSB PDB 8H0I · PDBe 8H0I · UniProt Q13951
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