Research workbench
Crystal structure of HIV-1 BG505 SOSIP.664 prefusion env trimer bound to small molecule HIV-1 entry inhibitor bms-626529 in complex with human antibodies PGT122 and 35O22 at 3.8 ångström
Analyse Crystal structure of HIV-1 BG505 SOSIP.664 prefusion env trimer bound to small… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U7O
- Type
- protein
- Length
- 1,461 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; 35O22 Fab heavy chain; 35O22 Fab light chain; PGT122 Fab…
- UniProt
- Q2N0S5
- Ligands
- 83J, NAG, MAN, BMA, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Envelope glycoprotein GP160 | protein | 126 | 57% helix, 7% strand | Q2N0S5 |
| D | 35O22 Fab heavy chain | protein | 242 | 4% helix, 46% strand | — |
| E | 35O22 Fab light chain | protein | 213 | 5% helix, 49% strand | — |
| G | Envelope glycoprotein GP160 | protein | 444 | 11% helix, 37% strand | Q2N0S5 |
| H | PGT122 Fab heavy chain | protein | 228 | 4% helix, 51% strand | — |
| L | PGT122 Fab light chain | protein | 208 | 5% helix, 45% strand | — |
Ligands and binding sites
- 83J · 1-[4-(benzenecarbonyl)piperazin-1-yl]-2-[4-methoxy-7-(3-methyl-1H-1,2,4-triazol-1-yl)-1H-pyrrolo[2,3-c]pyridin-3-yl]ethane-1,2-dione · ligand · chains G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 36 copies · chains B, D, G, H, L, E
- MAN · alpha-D-mannopyranose · sugar · 17 copies · chains D, E, H, G, L
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains D, E, H
- SO4 · Sulfate ion · ion · 5 copies · chains B, G, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 467 | 0.79 | 0.86 | 54 | NAG, 83J |
| 2 | 307 | 0.68 | 0.83 | 42 | empty |
| 3 | 59 | 0.65 | 0.94 | 26 | empty |
| 4 | 250 | 0.59 | 0.79 | 34 | empty |
| 5 | 203 | 0.57 | 0.80 | 38 | NAG |
Interfaces
8 interfaces between chains.
- B–G · 2668 Ų buried · 21 hydrogen bonds · protein-protein
- H–L · 2008 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1739 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 420 Ų buried · 6 hydrogen bonds · protein-protein
- G–L · 378 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 glycan, 21 disulfide (N-glycosylation, disulfide).
Compared structures
- 5U7O · Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule… · 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 Q2N0S5
- Elsewhere: RCSB PDB 5U7O · PDBe 5U7O · UniProt Q2N0S5
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