Research workbench
Cryo-EM structure of BG505 ds-sosip in complex with GLYCAN276- dependent broadly neutralizing antibody VRC40.01 Fab
Analyse Cryo-EM structure of BG505 ds-sosip in complex with GLYCAN276- dependent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LL1
- Type
- protein
- Length
- 3,135 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120; Envelope glycoprotein GP41; VRC40.01 Fab heavy chain…
- UniProt
- Q2N0S6, Q2N0S7
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 17% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | Envelope glycoprotein GP120 | protein | 449 | 14% helix, 40% strand | Q2N0S6 |
| B, D, I | Envelope glycoprotein GP41 | protein | 153 | 56% helix, 6% strand | Q2N0S7 |
| H, E, J | VRC40.01 Fab heavy chain | protein | 229 | 8% helix, 48% strand | — |
| L, F, K | VRC40.01 Fab light chain | protein | 214 | 5% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 69 copies · chains A, H, B, C, E, D, G, J, I
- BMA · beta-D-mannopyranose · sugar · 30 copies · chains A, H, L, B, E, F, D, J, K
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains H, L, E, F, J, K
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 | 341 | 0.83 | 0.93 | 46 | empty |
| 2 | 505 | 0.78 | 0.86 | 66 | empty |
| 3 | 368 | 0.77 | 0.87 | 56 | empty |
| 4 | 546 | 0.76 | 0.83 | 65 | empty |
| 5 | 733 | 0.76 | 0.81 | 76 | empty |
Interfaces
30 interfaces between chains.
- C–D · 3434 Ų buried · 37 hydrogen bonds · protein-protein
- G–I · 3365 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 3348 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 1906 Ų buried · 16 hydrogen bonds · protein-protein
- H–L · 1905 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 disulfide, 39 glycan (disulfide, N-glycosylation).
Compared structures
- 7LL1 · Cryo-EM structure of BG505 DS-SOSIP in complex with glycan276-dependent broadly… · 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
- Every structure of UniProt Q2N0S7
- Elsewhere: RCSB PDB 7LL1 · PDBe 7LL1 · UniProt Q2N0S6 · UniProt Q2N0S7
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