Research workbench
Cryo-EM model of HIV-1 env BG505 SOSIP.664 in complex with rabbit monoclonal antibody 11B fragment antigen binding variable domain
Analyse Cryo-EM model of HIV-1 env BG505 SOSIP.664 in complex with rabbit monoclonal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X98
- Type
- protein
- Length
- 2,367 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BG505 HIV-1 env GP120; BG505 HIV-1 env GP41; Monoclonal antibody 11B kappa chain…
- UniProt
- Q2N0S6
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 18% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | BG505 HIV-1 env GP120 | protein | 436 | 13% helix, 44% strand | Q2N0S6 |
| B, D, I | BG505 HIV-1 env GP41 | protein | 122 | 62% helix, 4% strand | Q2N0S6 |
| L, E, J | Monoclonal antibody 11B kappa chain | protein | 112 | 0% helix, 47% strand | — |
| H, F, K | Monoclonal antibody 11B fragment antigen binding heavy chain | protein | 119 | 5% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 60 copies · chains A, B, L, C, D, E, G, I, J
- BMA · beta-D-mannopyranose · sugar · 3 copies
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A, C, G
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 | 403 | 0.83 | 0.91 | 51 | empty |
| 2 | 279 | 0.71 | 0.85 | 52 | NAG |
| 3 | 307 | 0.70 | 0.84 | 52 | NAG |
| 4 | 318 | 0.70 | 0.83 | 60 | NAG |
| 5 | 91 | 0.69 | 0.93 | 27 | empty |
Interfaces
21 interfaces between chains.
- G–I · 2398 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 2398 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2395 Ų buried · 23 hydrogen bonds · protein-protein
- J–K · 1044 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1043 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 42 disulfide (N-glycosylation, disulfide).
Compared structures
- 6X98 · Cryo-EM model of HIV-1 Env BG505 SOSIP.664 in complex with rabbit monoclonal antibody 11B… · 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 6X98 · PDBe 6X98 · UniProt Q2N0S6
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