MolNFT v1 · #126791 · protein
The structure of the mature HIV-1 ca hexameric lattice with curvature parameters: TILT=23, twist=-6
5MDF · Gag protein: “The structure of the mature HIV-1 ca hexameric lattice with curvature parameters: TILT=23, twist=-6”. Electron microscopy, 11 pockets (best druggability 0.35). MolNFT v1 #126791 on GenesisL1: 3D structure, binding…
- PDB
- 5MDF
- Type
- protein
- Length
- 1,474 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gag protein
- UniProt
- A0A0K0V8J8, E9MJT0
- Pockets
- 11 · best druggability 0.35
Structure
electron microscopy · 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
11 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.35 | 0.73 | 30 | empty |
| 2 | 121 | 0.33 | 0.72 | 32 | empty |
| 3 | 91 | 0.31 | 0.73 | 28 | empty |
| 4 | 86 | 0.30 | 0.73 | 19 | empty |
| 5 | 95 | 0.30 | 0.72 | 25 | empty |
Interfaces
14 interfaces between chains.
- F–f · 63 Ų buried · 1 hydrogen bond · protein-protein
- E–J · 63 Ų buried · 1 hydrogen bond · protein-protein
- D–I · 62 Ų buried · 1 hydrogen bond · protein-protein
- B–b · 62 Ų buried · 1 hydrogen bond · protein-protein
- A–a · 54 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5MDF · The structure of the mature HIV-1 CA hexameric lattice with curvature parameters… · the same entry in another collection · chain J against J, 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 5MDF · PDBe 5MDF · UniProt A0A0K0V8J8 · UniProt E9MJT0
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