Research workbench
Cryo-electron microscopy of tubular arrays of HIV-1 gag resolves structures essential for immature virus assembly.
Analyse Cryo-electron microscopy of tubular arrays of HIV-1 gag resolves structures… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D1K
- Type
- protein
- Length
- 1,314 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gag protein
- UniProt
- Q5D0H3
- Pockets
- 10 · best druggability 0.47
Structure
electron microscopy · 1 distinct chain · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Gag protein | protein | 219 | 0% helix, 0% strand | Q5D0H3 |
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 | 258 | 0.47 | 0.73 | 56 | empty |
| 2 | 240 | 0.45 | 0.72 | 49 | empty |
| 3 | 207 | 0.44 | 0.73 | 53 | empty |
| 4 | 122 | 0.37 | 0.73 | 29 | empty |
| 5 | 99 | 0.34 | 0.73 | 24 | empty |
Interfaces
7 interfaces between chains.
- B–C · 183 Ų buried · 0 hydrogen bonds · protein-protein
- E–F · 158 Ų buried · 0 hydrogen bonds · protein-protein
- A–F · 100 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 82 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 69 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4D1K · Cryo-electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for… · 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 Q5D0H3
- Elsewhere: RCSB PDB 4D1K · PDBe 4D1K · UniProt Q5D0H3
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