Research workbench
Xfel crystal structure of a natively-glycosylated BG505 SOSIP.664 HIV- 1 envelope trimer in complex with the broadly-neutralizing antibodies BG18 and 35O22
Analyse Xfel crystal structure of a natively-glycosylated BG505 SOSIP.664 HIV- 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CH7
- Type
- protein
- Length
- 1,467 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP41; 35O22 heavy chain; 35O22 light chain; Envelope glycoprotein…
- UniProt
- Q2N0S7, Q2N0S6
- Ligands
- NAG, MAN, BMA, FUC, GAL
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 9% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Envelope glycoprotein GP41 | protein | 134 | 52% helix, 5% strand | Q2N0S7 |
| D | 35O22 heavy chain | protein | 226 | 1% helix, 28% strand | — |
| E | 35O22 light chain | protein | 213 | 5% helix, 29% strand | — |
| G | Envelope glycoprotein GP120 | protein | 452 | 11% helix, 33% strand | Q2N0S6 |
| Q | BG18 heavy chain | protein | 231 | 1% helix, 26% strand | — |
| R | BG18 light chain | protein | 211 | 2% helix, 21% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 33 copies · chains B, D, G, E, Q
- MAN · alpha-D-mannopyranose · sugar · 31 copies · chains D, E, G, R, Q
- BMA · beta-D-mannopyranose · sugar · 13 copies · chains D, E, Q
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains B, D, G
- GAL · beta-D-galactopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 500 | 0.76 | 0.84 | 66 | empty |
| 2 | 91 | 0.75 | 0.97 | 25 | empty |
| 3 | 158 | 0.74 | 0.92 | 28 | empty |
| 4 | 54 | 0.70 | 0.97 | 16 | empty |
| 5 | 61 | 0.70 | 0.96 | 21 | empty |
Interfaces
9 interfaces between chains.
- B–G · 3026 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 2046 Ų buried · 18 hydrogen bonds · protein-protein
- Q–R · 1935 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 443 Ų buried · 11 hydrogen bonds · protein-protein
- D–G · 330 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 glycan, 16 disulfide, 1 isopeptide (N-glycosylation, disulfide, glycosylation, glycation, isopeptide).
Compared structures
- 6CH7 · XFEL crystal structure of a natively-glycosylated BG505 SOSIP.664 HIV-1 Envelope Trimer… · 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 6CH7 · PDBe 6CH7 · UniProt Q2N0S7 · UniProt Q2N0S6
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