MolNFT v1 · #157260 · protein
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 3H109L and 35O22 at 2.9 ångström
6MTJ · Envelope glycoprotein GP160: “Crystal structure of HIV-1 BG505 SOSIP.664 prefusion env trimer bound to small molecule HIV-1 entry inhibitor…”. X-ray diffraction, 4 ligands (83G, NAG, MAN), 20 pockets (best druggability 0.79). MolNFT…
- PDB
- 6MTJ
- Type
- protein
- Length
- 1,243 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
- 83G, NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.79
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 | 2% helix, 45% strand | — |
| E | 35O22 scfv light chain portion | protein | 105 | 3% helix, 45% strand | — |
| G | Envelope glycoprotein GP160 | protein | 440 | 12% helix, 44% strand | Q2N0S6 |
| H | 3H109L Fab heavy chain | protein | 226 | 8% helix, 54% strand | — |
| L | 3H109L Fab light chain | protein | 211 | 7% helix, 43% 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 · 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 | 308 | 0.79 | 0.90 | 42 | NAG, 83G |
| 2 | 76 | 0.72 | 0.96 | 22 | empty |
| 3 | 69 | 0.69 | 0.95 | 25 | empty |
| 4 | 80 | 0.63 | 0.91 | 23 | empty |
| 5 | 234 | 0.55 | 0.78 | 31 | NAG |
Interfaces
8 interfaces between chains.
- B–G · 2819 Ų buried · 24 hydrogen bonds · protein-protein
- H–L · 1930 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 884 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 380 Ų buried · 6 hydrogen bonds · protein-protein
- G–H · 348 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide, 18 glycan (disulfide, N-glycosylation).
Compared structures
- 6MTJ · 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 6MTJ · PDBe 6MTJ · UniProt Q2N0S6
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