Research workbench
The structure of the mature HIV-1 ca hexameric lattice with curvature parameters: TILT=17, twist=-6
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
- 5MDB
- 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
- 12 · best druggability 0.37
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
12 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.37 | 0.72 | 37 | empty |
| 2 | 122 | 0.33 | 0.72 | 32 | empty |
| 3 | 110 | 0.33 | 0.73 | 25 | empty |
| 4 | 112 | 0.33 | 0.72 | 29 | empty |
| 5 | 115 | 0.32 | 0.72 | 32 | empty |
Interfaces
16 interfaces between chains.
- B–b · 70 Ų buried · 2 hydrogen bonds · protein-protein
- D–I · 69 Ų buried · 2 hydrogen bonds · protein-protein
- E–J · 64 Ų buried · 1 hydrogen bond · protein-protein
- F–f · 63 Ų buried · 1 hydrogen bond · protein-protein
- D–H · 61 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5MDB · The structure of the mature HIV-1 CA hexameric lattice with curvature parameters… · the same entry in another collection · chain C against C, 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 5MDB · PDBe 5MDB · UniProt A0A0K0V8J8 · UniProt E9MJT0
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