Research workbench
Crystal structure of HIV-1 BG505 SOSIP.664 prefusion env trimer bound to small molecule HIV-1 entry inhibitor bms-818251 in complex with human antibodies 3H109L and 35O22 at 3.1 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
- 6MU7
- Type
- protein
- Length
- 1,245 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; 35O22 scfv heavy chain portion; 35O22 scfv light chain…
- UniProt
- Q2N0S6
- Ligands
- JYY, NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 13% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Envelope glycoprotein GP160 | protein | 133 | 53% helix, 5% strand | Q2N0S6 |
| D | 35O22 scfv heavy chain portion | protein | 128 | 5% helix, 45% strand | — |
| E | 35O22 scfv light chain portion | protein | 105 | 3% helix, 42% strand | — |
| G | Envelope glycoprotein GP160 | protein | 442 | 13% helix, 44% strand | Q2N0S6 |
| H | 3H109L Fab heavy chain | protein | 226 | 8% helix, 52% strand | — |
| L | 3H109L Fab light chain | protein | 211 | 6% helix, 45% strand | — |
Ligands and binding sites
- JYY · 4-{3-[{4-[(R)-cyano(phenyl)methyl]piperidin-1-yl}(oxo) acetyl]-4-methoxy-1H-pyrrolo[2,3-c]pyridin-7-yl}-N-(2-hydroxyethyl)-1,3-thiazole-2-carboxamide · ligand · chains G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 26 copies · chains B, D, G, L, H, E
- MAN · alpha-D-mannopyranose · sugar · 10 copies · chains D, E, G, 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 | 298 | 0.78 | 0.90 | 43 | NAG, JYY |
| 2 | 106 | 0.72 | 0.93 | 27 | empty |
| 3 | 60 | 0.66 | 0.94 | 23 | empty |
| 4 | 109 | 0.60 | 0.87 | 26 | empty |
| 5 | 202 | 0.55 | 0.79 | 27 | NAG |
Interfaces
8 interfaces between chains.
- B–G · 2858 Ų buried · 28 hydrogen bonds · protein-protein
- H–L · 1913 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 890 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 380 Ų buried · 5 hydrogen bonds · protein-protein
- G–H · 345 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide, 19 glycan (disulfide, N-glycosylation).
Compared structures
- 6MU7 · 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 6MU7 · PDBe 6MU7 · UniProt Q2N0S6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.