Research workbench
Structure of CD4 mimetic M48U1 in complex with BG505 SOSIP.664 HIV-1 Env trimer and 17b Fab
Analyse Structure of CD4 mimetic M48U1 in complex with BG505 SOSIP.664 HIV-1 Env trimer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LOK
- Type
- protein
- Length
- 2,005 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.9
- Source
- Homo sapiens; Human immunodeficiency virus 1; SYNTHETIC CONSTRUCT
- Molecule
- Envelope glycoprotein BG505 SOSIP.664 gp120; Envelope Glycoprotein BG505 SOSIP.664 gp41…
- UniProt
- Q2N0S6
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · resolution 3.9 · 10 distinct chains · 18% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Envelope glycoprotein BG505 SOSIP.664 gp120 | protein | 358 | 12% helix, 27% strand | Q2N0S6 |
| D | Envelope Glycoprotein BG505 SOSIP.664 gp41 | protein | 126 | 49% helix, 6% strand | Q2N0S6 |
| A | Envelope glycoprotein BG505 SOSIP.664 gp120 | protein | 363 | 8% helix, 24% strand | Q2N0S6 |
| B | Envelope Glycoprotein BG505 SOSIP.664 gp41 | protein | 123 | 54% helix, 5% strand | Q2N0S6 |
| J | 17b Fab Light Chain | protein | 106 | 0% helix, 44% strand | — |
| K, M | 17b Fab Heavy Chain | protein | 129 | 5% helix, 44% strand | — |
| L | 17b Fab Light Chain | protein | 109 | 0% helix, 42% strand | — |
| G, H, I | M48U1 | protein | 27 | 33% helix, 22% strand | — |
| F | Envelope Glycoprotein BG505 SOSIP.664 gp41 | protein | 128 | 55% helix, 1% strand | Q2N0S6 |
| E | Envelope glycoprotein BG505 SOSIP.664 gp120 | protein | 353 | 11% helix, 21% strand | Q2N0S6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains C, A, E
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains C, A, E
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains C, A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.81 | 0.82 | 114 | empty |
| 2 | 947 | 0.78 | 0.80 | 110 | empty |
| 3 | 458 | 0.74 | 0.84 | 88 | empty |
| 4 | 54 | 0.67 | 0.95 | 21 | empty |
| 5 | 65 | 0.66 | 0.93 | 26 | empty |
Interfaces
20 interfaces between chains.
- A–B · 2390 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 2283 Ų buried · 9 hydrogen bonds · protein-protein
- J–K · 875 Ų buried · 2 hydrogen bonds · protein-protein
- L–M · 866 Ų buried · 2 hydrogen bonds · protein-protein
- A–G · 764 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 12 glycan, 6 modified, 3 d-amino (disulfide, N-glycosylation, nonstandard, D-amino acid, O-glycosylation).
Compared structures
- 7LOK · Structure of CD4 mimetic M48U1 in complex with BG505 SOSIP.664 HIV-1 env trimer and 17B… · the same entry in another collection · chain A against A, 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 7LOK · PDBe 7LOK · UniProt Q2N0S6
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