Research workbench
HIV-1 envelope glycoprotein BG505 SOSIP.664 expressed in HEK293F cells in complex with RM20A3 Fab
Analyse HIV-1 envelope glycoprotein BG505 SOSIP.664 expressed in HEK293F cells in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X9R
- Type
- protein
- Length
- 786 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 envelope glycoprotein BG505 SOSIP.664 GP120; HIV-1 envelope glycoprotein BG505…
- UniProt
- Q2N0S6
- Ligands
- NAG, BMA, MAN
- Pockets
- 12 · best druggability 0.71
Structure
electron microscopy · 4 distinct chains · 19% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 envelope glycoprotein BG505 SOSIP.664 GP120 | protein | 432 | 14% helix, 45% strand | Q2N0S6 |
| B | HIV-1 envelope glycoprotein BG505 SOSIP.664 GP41 | protein | 121 | 58% helix, 4% strand | Q2N0S6 |
| H | RM20A3 Fab heavy chain | protein | 124 | 7% helix, 50% strand | — |
| L | RM20A3 Fab light chain | protein | 109 | 7% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 27 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.71 | 0.83 | 67 | NAG |
| 2 | 65 | 0.67 | 0.95 | 25 | empty |
| 3 | 75 | 0.54 | 0.86 | 20 | empty |
| 4 | 204 | 0.51 | 0.76 | 33 | empty |
| 5 | 119 | 0.45 | 0.78 | 21 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2359 Ų buried · 20 hydrogen bonds · protein-protein
- H–L · 907 Ų buried · 3 hydrogen bonds · protein-protein
- A–H · 170 Ų buried · 3 hydrogen bonds · protein-protein
- B–H · 167 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 glycan, 12 disulfide (N-glycosylation, disulfide).
Compared structures
- 6X9R · HIV-1 Envelope Glycoprotein BG505 SOSIP.664 expressed in HEK293F cells in complex with… · the same entry in another collection · chain A against A, 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 6X9R · PDBe 6X9R · UniProt Q2N0S6
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