Research workbench
Crystal structure at 3.7 a resolution of fully glycosylated HIV-1 clade B jr-fl SOSIP.664 prefusion env trimer in complex with broadly neutralizing antibodies PGT122, 35O22 and VRC01
Analyse Crystal structure at 3.7 a resolution of fully glycosylated HIV-1 clade B jr-fl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FYK
- Type
- protein
- Length
- 1,712 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Jr-fl, GP41 env ectodomain; 35O22; Jr-fl, GP120 env ectodomain; PGT122; VRC01
- UniProt
- Q6BC19, Q75760
- Ligands
- MAN, NAG, BMA
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 8 distinct chains · 11% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Jr-fl, GP41 env ectodomain | protein | 151 | 56% helix, 5% strand | Q6BC19 |
| D | 35O22 | protein | 242 | 1% helix, 36% strand | — |
| E | 35O22 | protein | 213 | 5% helix, 42% strand | — |
| G | Jr-fl, GP120 env ectodomain | protein | 451 | 14% helix, 41% strand | Q75760 |
| H | PGT122 | protein | 228 | 5% helix, 45% strand | — |
| L | PGT122 | protein | 210 | 4% helix, 40% strand | — |
| U | VRC01 | protein | 119 | 3% helix, 44% strand | — |
| V | VRC01 | protein | 98 | 3% helix, 33% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 67 copies · chains D, E, L, G, V, H, U
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 45 copies · chains B, D, G, L, V, H, U
- BMA · beta-D-mannopyranose · sugar · 18 copies · chains D, E, V, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.75 | 0.87 | 51 | NAG |
| 2 | 53 | 0.68 | 0.97 | 21 | empty |
| 3 | 313 | 0.67 | 0.82 | 36 | NAG |
| 4 | 232 | 0.67 | 0.84 | 29 | empty |
| 5 | 310 | 0.67 | 0.82 | 42 | empty |
Interfaces
12 interfaces between chains.
- B–G · 3032 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 2099 Ų buried · 24 hydrogen bonds · protein-protein
- H–L · 1887 Ų buried · 14 hydrogen bonds · protein-protein
- G–U · 1016 Ų buried · 23 hydrogen bonds · protein-protein
- U–V · 779 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 glycan, 23 disulfide (N-glycosylation, disulfide).
Compared structures
- 5FYK · Crystal Structure at 3.7 A Resolution of Fully Glycosylated HIV-1 Clade B JR-FL 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 Q6BC19
- Every structure of UniProt Q75760
- Elsewhere: RCSB PDB 5FYK · PDBe 5FYK · UniProt Q6BC19 · UniProt Q75760
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.