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Crystal structure of the cleavage-independent prefusion HIV env glycoprotein trimer of the clade a BG505 isolate (nfl construct) in complex with fabs PGT122 and PGV19 at 3.39 a
Analyse Crystal structure of the cleavage-independent prefusion HIV env glycoprotein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B0N
- Type
- protein
- Length
- 1,405 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PGV19 Fab heavy chain; PGV19 light chain; Envelope glycoprotein GP140; PGT122 Fab heavy…
- UniProt
- Q2N0S6, Q2N0S9
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | PGV19 Fab heavy chain | protein | 171 | 4% helix, 41% strand | — |
| E | PGV19 light chain | protein | 182 | 6% helix, 38% strand | — |
| G | Envelope glycoprotein GP140 | protein | 610 | 21% helix, 28% strand | Q2N0S6, Q2N0S9 |
| H | PGT122 Fab heavy chain | protein | 232 | 1% helix, 49% strand | — |
| L | PGT122 light chain | protein | 210 | 6% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 36 copies · chains G, L, D, E, H
- MAN · alpha-D-mannopyranose · sugar · 32 copies · chains L, G, E, H
- BMA · beta-D-mannopyranose · sugar · 10 copies · chains 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.76 | 0.81 | 63 | empty |
| 2 | 59 | 0.69 | 0.97 | 21 | empty |
| 3 | 59 | 0.64 | 0.93 | 18 | empty |
| 4 | 147 | 0.63 | 0.86 | 22 | empty |
| 5 | 430 | 0.62 | 0.77 | 38 | empty |
Interfaces
6 interfaces between chains.
- H–L · 2069 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1318 Ų buried · 11 hydrogen bonds · protein-protein
- D–G · 965 Ų buried · 12 hydrogen bonds · protein-protein
- E–G · 432 Ų buried · 5 hydrogen bonds · protein-protein
- G–H · 391 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 glycan, 17 disulfide (N-glycosylation, disulfide).
Compared structures
- 6B0N · Crystal structure of the cleavage-independent prefusion HIV Env glycoprotein trimer of… · the same entry in another collection · chain D against D, 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
- Every structure of UniProt Q2N0S9
- Elsewhere: RCSB PDB 6B0N · PDBe 6B0N · UniProt Q2N0S6 · UniProt Q2N0S9
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