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Pre-fusion structure of trimeric HIV-1 envelope glycoprotein determined by cryo-electron microscopy
Analyse Pre-fusion structure of trimeric HIV-1 envelope glycoprotein determined by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CC8
- Type
- protein
- Length
- 2,430 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GP41; GP120; Monoclonal antibody VRC03 Fab heavy chain; Monoclonal antibody VRC03 Fab…
- Pockets
- 20 · best druggability 0.73
Structure
electron microscopy · 4 distinct chains · 15% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | GP41 | protein | 31 | 94% helix, 0% strand | — |
| D, E, G | GP120 | protein | 344 | 19% helix, 39% strand | — |
| F, H, I | Monoclonal antibody VRC03 Fab heavy chain | protein | 227 | 9% helix, 51% strand | — |
| J, K, L | Monoclonal antibody VRC03 Fab light chain | protein | 208 | 5% helix, 51% strand | — |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 590 | 0.73 | 0.80 | 55 | empty |
| 2 | 609 | 0.72 | 0.80 | 52 | empty |
| 3 | 590 | 0.72 | 0.80 | 52 | empty |
| 4 | 380 | 0.57 | 0.75 | 47 | empty |
| 5 | 346 | 0.56 | 0.75 | 45 | empty |
Interfaces
15 interfaces between chains.
- F–J · 1725 Ų buried · 11 hydrogen bonds · protein-protein
- H–L · 1723 Ų buried · 11 hydrogen bonds · protein-protein
- I–K · 1721 Ų buried · 11 hydrogen bonds · protein-protein
- E–H · 1060 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 1058 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 4CC8 · Pre-fusion structure of trimeric HIV-1 envelope glycoprotein determined by cryo-electron… · 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
- Elsewhere: RCSB PDB 4CC8 · PDBe 4CC8
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