Research workbench
Crystal structure of HIV-1 BG505 SOSIP.664 prefusion env trimer bound to small molecule HIV-1 entry inhibitor bms-378806 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
- 5U7M
- Type
- protein
- Length
- 1,459 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
- 83G, 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, 6% strand | Q2N0S5 |
| D | 35O22 Fab heavy chain | protein | 242 | 4% helix, 47% strand | — |
| E | 35O22 Fab light chain | protein | 213 | 3% helix, 47% strand | — |
| G | Envelope glycoprotein GP160 | protein | 442 | 13% helix, 38% strand | Q2N0S5 |
| H | PGT122 Fab heavy chain | protein | 228 | 4% helix, 50% strand | — |
| L | PGT122 Fab light chain | protein | 208 | 5% helix, 44% strand | — |
Ligands and binding sites
- 83G · 1-[(2R)-4-(benzenecarbonyl)-2-methylpiperazin-1-yl]-2-(4-methoxy-1H-pyrrolo[2,3-b]pyridin-3-yl)ethane-1,2-dione · ligand · chains G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 35 copies · chains B, D, G, H, L, E
- MAN · alpha-D-mannopyranose · sugar · 16 copies · chains D, E, G, H, L
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains D, E, H, G
- 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.79 | 0.89 | 37 | NAG, 83G |
| 2 | 61 | 0.65 | 0.94 | 27 | empty |
| 3 | 191 | 0.63 | 0.83 | 25 | empty |
| 4 | 73 | 0.59 | 0.89 | 17 | empty |
| 5 | 487 | 0.58 | 0.73 | 56 | empty |
Interfaces
8 interfaces between chains.
- B–G · 2744 Ų buried · 24 hydrogen bonds · protein-protein
- H–L · 2023 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1721 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 427 Ų buried · 6 hydrogen bonds · protein-protein
- G–L · 379 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 glycan, 21 disulfide (N-glycosylation, disulfide).
Compared structures
- 5U7M · 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 5U7M · PDBe 5U7M · UniProt Q2N0S5
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