Research workbench
The structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=29, twist=0
Analyse The structure of the mature HIV-1 CA hexameric lattice with curvature… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MDG
- Type
- protein
- Length
- 1,474 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 8.7
- Source
- Human immunodeficiency virus 1
- Molecule
- Gag protein
- UniProt
- A0A0K0V8J8, E9MJT0
- Pockets
- 13 · best druggability 0.36
Structure
electron microscopy · resolution 8.7 · 2 distinct chains · 60% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F, W, C, D, E, G | Gag protein | protein | 74 | 64% helix, 0% strand | A0A0K0V8J8 |
| a, b, f, H, I, J | Gag protein | protein | 147 | 58% helix, 4% strand | E9MJT0 |
Pockets
13 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.36 | 0.72 | 34 | empty |
| 2 | 126 | 0.34 | 0.73 | 25 | empty |
| 3 | 124 | 0.33 | 0.72 | 30 | empty |
| 4 | 110 | 0.33 | 0.73 | 26 | empty |
| 5 | 107 | 0.32 | 0.73 | 26 | empty |
Interfaces
16 interfaces between chains.
- E–J · 62 Ų buried · 1 hydrogen bond · protein-protein
- F–f · 60 Ų buried · 1 hydrogen bond · protein-protein
- B–b · 60 Ų buried · 2 hydrogen bonds · protein-protein
- D–I · 59 Ų buried · 2 hydrogen bonds · protein-protein
- D–H · 57 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5MDG · The structure of the mature HIV-1 ca hexameric lattice with curvature parameters… · the same entry in another collection · chain A against A, 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 A0A0K0V8J8
- Every structure of UniProt E9MJT0
- Elsewhere: RCSB PDB 5MDG · PDBe 5MDG · UniProt A0A0K0V8J8 · UniProt E9MJT0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.