Research workbench
Cryo-EM structure of the BG505 SOSIP.664 HIV-1 env trimer with 3 PGV04 fabs
Analyse Cryo-EM structure of the BG505 SOSIP.664 HIV-1 env trimer with 3 PGV04 fabs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J5M
- Type
- protein
- Length
- 2,733 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BG505 sosip GP120; BG505 sosip GP41; PGV04 light chain; PGV04 heavy chain
- UniProt
- Q2N0S6
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 17% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | BG505 sosip GP120 | protein | 415 | 14% helix, 31% strand | Q2N0S6 |
| B, F, J | BG505 sosip GP41 | protein | 63 | 94% helix, 0% strand | — |
| C, G, K | PGV04 light chain | protein | 208 | 7% helix, 49% strand | — |
| D, H, L | PGV04 heavy chain | protein | 225 | 9% helix, 48% strand | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.83 | 0.89 | 68 | empty |
| 2 | 705 | 0.81 | 0.85 | 81 | empty |
| 3 | 250 | 0.76 | 0.90 | 35 | empty |
| 4 | 624 | 0.76 | 0.82 | 82 | empty |
| 5 | 316 | 0.76 | 0.88 | 46 | empty |
Interfaces
21 interfaces between chains.
- C–D · 1966 Ų buried · 13 hydrogen bonds · protein-protein
- K–L · 1963 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 1962 Ų buried · 13 hydrogen bonds · protein-protein
- E–H · 961 Ų buried · 16 hydrogen bonds · protein-protein
- I–L · 959 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide (disulfide).
Compared structures
- 3J5M · Cryo-EM structure of the BG505 SOSIP.664 HIV-1 Env trimer with 3 PGV04 Fabs · 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 Q2N0S6
- Elsewhere: RCSB PDB 3J5M · PDBe 3J5M · UniProt Q2N0S6
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