Research workbench
3.9 ångström crystal structure of a fully and natively glycosylated BG505 SOSIP.664 HIV-1 env trimer in complex with the broadly neutralizing antibodies ioma and 10-1074.
Analyse 3.9 ångström crystal structure of a fully and natively glycosylated BG505… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T3X
- Type
- protein
- Length
- 1,455 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; 10-1074 heavy chain; 10-1074 light chain; Ioma heavy chain…
- UniProt
- Q2N0S6
- Ligands
- NAG, MAN, BMA, GAL, FUC, SIA
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Envelope glycoprotein GP160 | protein | 126 | 49% helix, 2% strand | Q2N0S6 |
| G | Envelope glycoprotein GP160 | protein | 449 | 12% helix, 35% strand | Q2N0S6 |
| H | 10-1074 heavy chain | protein | 230 | 5% helix, 49% strand | — |
| L | 10-1074 light chain | protein | 211 | 5% helix, 45% strand | — |
| D | Ioma heavy chain | protein | 229 | 3% helix, 42% strand | — |
| E | Ioma light chain | protein | 210 | 9% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 51 copies · chains B, G, D, E, L, H
- MAN · alpha-D-mannopyranose · sugar · 31 copies · chains G, E, L, H, D
- BMA · beta-D-mannopyranose · sugar · 13 copies · chains D, H
- GAL · beta-D-galactopyranose · sugar · 9 copies
- FUC · alpha-L-fucopyranose · sugar · 7 copies · chains B, G, D
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 368 | 0.78 | 0.88 | 51 | FUC |
| 2 | 641 | 0.76 | 0.82 | 87 | empty |
| 3 | 330 | 0.66 | 0.81 | 39 | empty |
| 4 | 112 | 0.63 | 0.87 | 27 | empty |
| 5 | 297 | 0.61 | 0.79 | 23 | empty |
Interfaces
7 interfaces between chains.
- B–G · 2588 Ų buried · 26 hydrogen bonds · protein-protein
- H–L · 2087 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1894 Ų buried · 20 hydrogen bonds · protein-protein
- G–D · 924 Ų buried · 15 hydrogen bonds · protein-protein
- G–L · 310 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide, 19 glycan (disulfide, N-glycosylation).
Compared structures
- 5T3X · 3.9 Angstrom Crystal Structure of a Fully and Natively Glycosylated BG505 SOSIP.664 HIV-1… · 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 5T3X · PDBe 5T3X · UniProt Q2N0S6
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