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Crystal structure at 3.7 a resolution of fully glycosylated HIV-1 clade a BG505 SOSIP.664 prefusion env trimer in complex with broadly neutralizing antibodies PGT122 and 35O22
Analyse Crystal structure at 3.7 a resolution of fully glycosylated HIV-1 clade a BG505… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FYL
- Type
- protein
- Length
- 1,472 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BG505 GP120 env ectodomain; 35O22 antibody Fab heavy chain; 35O22 antibody Fab light…
- UniProt
- Q2N0S6
- Ligands
- MAN, NAG, BMA
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 12% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | BG505 GP120 env ectodomain | protein | 126 | 52% helix, 6% strand | Q2N0S6 |
| D | 35O22 antibody Fab heavy chain | protein | 242 | 7% helix, 36% strand | — |
| E | 35O22 antibody Fab light chain | protein | 213 | 1% helix, 40% strand | — |
| G | BG505 GP120 env ectodomain | protein | 453 | 14% helix, 39% strand | Q2N0S6 |
| H | PGT122 antibody Fab heavy chain | protein | 228 | 7% helix, 42% strand | — |
| L | PGT122 antibody Fab light chain | protein | 210 | 7% helix, 42% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 57 copies · chains D, E, H, L, G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 40 copies · chains B, D, G, H, L, E
- BMA · beta-D-mannopyranose · sugar · 17 copies · chains D, E, H, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.73 | 0.84 | 58 | NAG |
| 2 | 283 | 0.69 | 0.84 | 36 | empty |
| 3 | 283 | 0.69 | 0.83 | 47 | empty |
| 4 | 588 | 0.61 | 0.74 | 68 | empty |
| 5 | 230 | 0.54 | 0.77 | 35 | empty |
Interfaces
8 interfaces between chains.
- B–G · 2573 Ų buried · 21 hydrogen bonds · protein-protein
- H–L · 2049 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 2000 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 408 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 356 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 glycan, 21 disulfide (N-glycosylation, disulfide).
Compared structures
- 5FYL · Crystal Structure at 3.7 A Resolution of Fully Glycosylated HIV-1 Clade A BG505 SOSIP.664… · the same entry in another collection · chain B against B, 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 5FYL · PDBe 5FYL · UniProt Q2N0S6
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