Research workbench
Crystal structure at 3.7 a resolution of glycosylated HIV-1 clade a BG505 SOSIP.664 prefusion env trimer with four glycans (N197, N276, N362, and N462) removed in complex with neutralizing antibodies 3H+109L and 35O22.
Analyse Crystal structure at 3.7 a resolution of 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
- 5V7J
- Type
- protein
- Length
- 1,495 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; Antibody 3H+109L Fab light chain; Antibody 3H+109L Fab heavy…
- UniProt
- Q2N0S6
- Ligands
- MAN, NAG, BMA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP160 | protein | 452 | 11% helix, 30% strand | Q2N0S6 |
| B | Envelope glycoprotein GP160 | protein | 148 | 49% helix, 2% strand | Q2N0S6 |
| L | Antibody 3H+109L Fab light chain | protein | 211 | 6% helix, 27% strand | — |
| H | Antibody 3H+109L Fab heavy chain | protein | 231 | 5% helix, 37% strand | — |
| D | Antibody 35O22 Fab light chain | protein | 240 | 5% helix, 29% strand | — |
| E | Antibody 35O22 Fab heavy chain | protein | 213 | 3% helix, 25% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 39 copies · chains D, E, L, G, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 29 copies · chains G, B, D, L, H, E
- BMA · beta-D-mannopyranose · sugar · 11 copies · chains D, E, 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.79 | 0.94 | 30 | empty |
| 2 | 765 | 0.75 | 0.80 | 88 | empty |
| 3 | 591 | 0.74 | 0.81 | 76 | empty |
| 4 | 115 | 0.74 | 0.94 | 22 | empty |
| 5 | 350 | 0.74 | 0.85 | 64 | NAG |
Interfaces
9 interfaces between chains.
- G–B · 2737 Ų buried · 18 hydrogen bonds · protein-protein
- L–H · 1933 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1439 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 355 Ų buried · 5 hydrogen bonds · protein-protein
- G–L · 318 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 5V7J · Crystal Structure at 3.7 A Resolution of Glycosylated HIV-1 Clade A BG505 SOSIP.664… · the same entry in another collection · chain G against G, 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 5V7J · PDBe 5V7J · UniProt Q2N0S6
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