Research workbench
BG505 SOSIP.664 in complex with the V3-targeting rhesus macaque antibody 1485 and human gp120-gp41 interface antibody 8ANC195
Analyse BG505 SOSIP.664 in complex with the V3-targeting rhesus macaque antibody 1485… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KDE
- Type
- protein
- Length
- 3,069 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.55
- Source
- Homo sapiens; Human immunodeficiency virus 1
- Molecule
- HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41; Envelope glycoprotein gp120; Ab 1485…
- UniProt
- Q2N0S6
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · resolution 3.55 · 6 distinct chains · 10% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41 | protein | 123 | 49% helix, 6% strand | Q2N0S6 |
| E, F, G | Envelope glycoprotein gp120 | protein | 429 | 7% helix, 34% strand | Q2N0S6 |
| H, J, M | Ab 1485 Heavy Chain | protein | 129 | 0% helix, 29% strand | — |
| O, Q, S | 8ANC195 Fab Heavy Chain | protein | 132 | 2% helix, 48% strand | — |
| P, R, T | 8ANC195 Fab Light Chain | protein | 107 | 3% helix, 31% strand | — |
| I, L, N | Ab 1485 Light Chain | protein | 103 | 3% helix, 32% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 82 copies · chains A, T, S, B, P, O, C, R, Q, E, M, F, J, G, H
- MAN · alpha-D-mannopyranose · sugar · 35 copies · chains M, S, N, Q, J, I, H, O, L
- BMA · beta-D-mannopyranose · sugar · 15 copies · chains T, R, M, S, J, Q, H, O
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.83 | 0.90 | 56 | empty |
| 2 | 374 | 0.69 | 0.82 | 58 | NAG |
| 3 | 78 | 0.69 | 0.95 | 27 | empty |
| 4 | 296 | 0.69 | 0.83 | 46 | NAG |
| 5 | 61 | 0.68 | 0.96 | 20 | empty |
Interfaces
30 interfaces between chains.
- B–G · 2579 Ų buried · 20 hydrogen bonds · protein-protein
- C–F · 2563 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 2556 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1018 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 998 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 58 glycan, 45 disulfide (N-glycosylation, disulfide).
Compared structures
- 7KDE · BG505 SOSIP.664 in complex with the V3-targeting rhesus macaque antibody 1485 and human… · 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 7KDE · PDBe 7KDE · UniProt Q2N0S6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.