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Crystal Structure of HIV-1 B41 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor BMS-386150 in Complex with Human Antibodies 3H109L and 35O22 at 3.8 Angstrom
Analyse Crystal Structure of HIV-1 B41 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
- 6MUG
- Type
- protein
- Length
- 1,225 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.954
- Source
- Homo sapiens; Human immunodeficiency virus 1
- Molecule
- Envelope glycoprotein gp160; 35O22 scFv heavy chain portion; 35O22 scFv light chain…
- UniProt
- B3UEZ6, B3UES2
- Ligands
- JYS, NAG, MAN, BMA
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.954 · 6 distinct chains · 11% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Envelope glycoprotein gp160 | protein | 123 | 54% helix, 7% strand | B3UEZ6 |
| D | 35O22 scFv heavy chain portion | protein | 128 | 5% helix, 38% strand | — |
| E | 35O22 scFv light chain portion | protein | 112 | 3% helix, 42% strand | — |
| G | Envelope glycoprotein gp160 | protein | 424 | 10% helix, 42% strand | B3UES2 |
| H | 3H109L Fab heavy chain | protein | 227 | 5% helix, 44% strand | — |
| L | 3H109L Fab light chain | protein | 211 | 5% helix, 39% strand | — |
Ligands and binding sites
- JYS · 1-[4-(benzenecarbonyl)piperazin-1-yl]-2-(4-bromo-7-fluoro-1H-indol-3-yl)ethane-1,2-dione · ligand · chains G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains B, D, G, L, H
- MAN · alpha-D-mannopyranose · sugar · 10 copies · chains D, E, G, H, L
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains D, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.77 | 0.86 | 54 | NAG, JYS |
| 2 | 61 | 0.68 | 0.96 | 27 | empty |
| 3 | 219 | 0.59 | 0.80 | 20 | empty |
| 4 | 228 | 0.58 | 0.79 | 35 | empty |
| 5 | 135 | 0.53 | 0.81 | 21 | empty |
Interfaces
8 interfaces between chains.
- B–G · 2630 Ų buried · 21 hydrogen bonds · protein-protein
- H–L · 1968 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 983 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 396 Ų buried · 5 hydrogen bonds · protein-protein
- G–H · 302 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide, 18 glycan (disulfide, N-glycosylation).
Compared structures
- 6MUG · Crystal structure of HIV-1 B41 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 B3UEZ6
- Every structure of UniProt B3UES2
- Elsewhere: RCSB PDB 6MUG · PDBe 6MUG · UniProt B3UEZ6 · UniProt B3UES2
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