MolNFT v1 · #126789 · protein
The structure of the mature HIV-1 ca hexameric lattice with curvature parameters: TILT=23, TWIST=6
5MDD · Gag protein: “The structure of the mature HIV-1 ca hexameric lattice with curvature parameters: TILT=23, TWIST=6”. Electron microscopy, 10 pockets (best druggability 0.36). MolNFT v1 #126789 on GenesisL1: 3D structure, binding sites…
- PDB
- 5MDD
- 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
- 10 · best druggability 0.36
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
10 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.36 | 0.72 | 31 | empty |
| 2 | 128 | 0.34 | 0.72 | 25 | empty |
| 3 | 112 | 0.32 | 0.72 | 26 | empty |
| 4 | 103 | 0.31 | 0.72 | 27 | empty |
| 5 | 104 | 0.31 | 0.72 | 29 | empty |
Interfaces
14 interfaces between chains.
- C–H · 68 Ų buried · 2 hydrogen bonds · protein-protein
- A–a · 68 Ų buried · 2 hydrogen bonds · protein-protein
- E–J · 65 Ų buried · 1 hydrogen bond · protein-protein
- F–f · 64 Ų buried · 1 hydrogen bond · protein-protein
- D–I · 61 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5MDD · The structure of the mature HIV-1 CA hexameric lattice with curvature parameters… · the same entry in another collection · chain f against f, 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 5MDD · PDBe 5MDD · UniProt A0A0K0V8J8 · UniProt E9MJT0
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