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Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor Compound 484 in Complex with Human Antibodies 3H109L and 35O22 at 3.0 Angstrom
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
- 6MTN
- Type
- protein
- Length
- 1,237 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Homo sapiens; Human immunodeficiency virus 1
- Molecule
- Envelope glycoprotein gp160; 35O22 scFv heavy chain portion; 35O22 scFv light chain…
- UniProt
- Q2N0S6
- Ligands
- JYJ, NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.5 · 6 distinct chains · 13% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Envelope glycoprotein gp160 | protein | 128 | 55% helix, 7% strand | Q2N0S6 |
| D | 35O22 scFv heavy chain portion | protein | 128 | 5% helix, 46% strand | — |
| E | 35O22 scFv light chain portion | protein | 105 | 3% helix, 39% strand | — |
| G | Envelope glycoprotein gp160 | protein | 439 | 13% helix, 43% strand | Q2N0S6 |
| H | 3H109L Fab heavy chain | protein | 226 | 7% helix, 51% strand | — |
| L | 3H109L Fab light chain | protein | 211 | 6% helix, 48% strand | — |
Ligands and binding sites
- JYJ · {4-[1-(3-chlorophenyl)cyclopropane-1-carbonyl]piperazin-1-yl}(thiophen-3-yl)methanone · ligand · chains G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 27 copies · chains D, B, G, H, E
- MAN · alpha-D-mannopyranose · sugar · 10 copies · chains D, E, H, L
- BMA · beta-D-mannopyranose · sugar · 4 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.78 | 0.87 | 49 | NAG, JYJ |
| 2 | 119 | 0.77 | 0.96 | 32 | empty |
| 3 | 62 | 0.65 | 0.94 | 24 | empty |
| 4 | 226 | 0.62 | 0.82 | 38 | empty |
| 5 | 257 | 0.56 | 0.77 | 30 | NAG |
Interfaces
9 interfaces between chains.
- B–G · 2768 Ų buried · 25 hydrogen bonds · protein-protein
- H–L · 1938 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 886 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 389 Ų buried · 6 hydrogen bonds · protein-protein
- G–H · 351 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 glycan, 18 disulfide (N-glycosylation, disulfide).
Compared structures
- 6MTN · 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 Q2N0S6
- Elsewhere: RCSB PDB 6MTN · PDBe 6MTN · UniProt Q2N0S6
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