Research workbench
Initial contact of HIV-1 env with CD4: cryo-EM structure of BG505 ds- sosip trimer in complex with CD4 and antibody PGT145
Analyse Initial contact of HIV-1 env with CD4: cryo-EM structure of BG505 ds- sosip… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U1F
- Type
- protein
- Length
- 2,549 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BG505 ds-sosip GP120; BG505 sosip GP41; PGT145 heavy chain; PGT145 light chain; T-cell…
- UniProt
- Q2N0S6, P01730
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 14% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, A | BG505 ds-sosip GP120 | protein | 447 | 13% helix, 37% strand | Q2N0S6 |
| B, E, F | BG505 sosip GP41 | protein | 132 | 57% helix, 0% strand | Q2N0S6 |
| H | PGT145 heavy chain | protein | 235 | 12% helix, 51% strand | — |
| L | PGT145 light chain | protein | 214 | 6% helix, 51% strand | — |
| M | T-cell surface glycoprotein CD4 | protein | 363 | 5% helix, 51% strand | P01730 |
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 | 830 | 0.83 | 0.86 | 132 | empty |
| 2 | 807 | 0.83 | 0.86 | 133 | empty |
| 3 | 1144 | 0.78 | 0.81 | 99 | empty |
| 4 | 636 | 0.77 | 0.83 | 110 | empty |
| 5 | 422 | 0.77 | 0.86 | 76 | empty |
Interfaces
12 interfaces between chains.
- C–E · 865 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 809 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 749 Ų buried · 3 hydrogen bonds · protein-protein
- H–L · 663 Ų buried · 2 hydrogen bonds · protein-protein
- D–M · 158 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (sulfation).
Compared structures
- 5U1F · Initial contact of HIV-1 Env with CD4: Cryo-EM structure of BG505 DS-SOSIP trimer in… · the same entry in another collection · chain M against M, TM-score 1.00
- P01730 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD4 (P01730) · a predicted model of the same protein · chain M against A, TM-score 0.96
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
- Every structure of UniProt P01730
- Elsewhere: RCSB PDB 5U1F · PDBe 5U1F · UniProt Q2N0S6 · UniProt P01730
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