MolNFT v1 · #146327 · protein
Crystal structure at 4.3 a resolution of glycosylated HIV-1 clade a BG505 SOSIP.664 prefusion env trimer with interdomain stabilization 113C-429GCG in complex with broadly neutralizing antibodies PGT122 and 35O22
6DE7 · Envelope glycoprotein GP160: “Crystal structure at 4.3 a resolution of glycosylated HIV-1 clade a BG505 SOSIP.664 prefusion env trimer with…”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 17 pockets (best druggability 0.71). MolNFT…
- PDB
- 6DE7
- Type
- protein
- Length
- 1,415 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; 35O22 heavy chain; 35O22 light chain; PGT122 heavy chain…
- UniProt
- Q2N0S7, Q2N0S6
- Ligands
- NAG, MAN, BMA, SO4
- Pockets
- 17 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 12% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Envelope glycoprotein GP160 | protein | 129 | 61% helix, 7% strand | Q2N0S7 |
| D | 35O22 heavy chain | protein | 205 | 4% helix, 45% strand | — |
| E | 35O22 light chain | protein | 194 | 3% helix, 48% strand | — |
| G | Envelope glycoprotein GP160 | protein | 453 | 12% helix, 35% strand | Q2N0S6 |
| H | PGT122 heavy chain | protein | 226 | 7% helix, 53% strand | — |
| L | PGT122 light chain | protein | 208 | 6% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 36 copies · chains B, D, G, H, L, E
- MAN · alpha-D-mannopyranose · sugar · 16 copies · chains D, E, H, G, L
- BMA · beta-D-mannopyranose · sugar · 7 copies · chains D, E, H
- SO4 · Sulfate ion · ion · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.71 | 0.86 | 45 | NAG |
| 2 | 197 | 0.61 | 0.82 | 31 | empty |
| 3 | 282 | 0.57 | 0.77 | 34 | empty |
| 4 | 416 | 0.54 | 0.73 | 58 | empty |
| 5 | 125 | 0.54 | 0.82 | 25 | empty |
Interfaces
8 interfaces between chains.
- B–G · 2763 Ų buried · 17 hydrogen bonds · protein-protein
- H–L · 2018 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1589 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 430 Ų buried · 6 hydrogen bonds · protein-protein
- G–L · 369 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 21 glycan (disulfide, N-glycosylation).
Compared structures
- 6DE7 · Crystal Structure at 4.3 A Resolution of Glycosylated HIV-1 Clade A BG505 SOSIP.664… · 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 Q2N0S7
- Every structure of UniProt Q2N0S6
- Elsewhere: RCSB PDB 6DE7 · PDBe 6DE7 · UniProt Q2N0S7 · UniProt Q2N0S6
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