Research workbench
Cryo-EM structure of BG505 ds-sosip in complex with GLYCAN276- dependent broadly neutralizing antibody VRC33.01 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
- 7LL2
- Type
- protein
- Length
- 3,060 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120; Envelope glycoprotein GP41; VRC33.01 Fab heavy chain…
- UniProt
- Q2N0S6, Q2N0S7
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 4 distinct chains · 16% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Envelope glycoprotein GP120 | protein | 447 | 13% helix, 39% strand | Q2N0S6 |
| B, D, F | Envelope glycoprotein GP41 | protein | 136 | 61% helix, 4% strand | Q2N0S7 |
| H, I, K | VRC33.01 Fab heavy chain | protein | 220 | 4% helix, 50% strand | — |
| L, J, M | VRC33.01 Fab light chain | protein | 217 | 6% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 78 copies · chains A, B, E, H, C, D, I, F, K
- BMA · beta-D-mannopyranose · sugar · 30 copies · chains L, H, I, M, K
- MAN · alpha-D-mannopyranose · sugar · 24 copies · chains H, L, C, I, J, E, K, M
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 | 244 | 0.80 | 0.93 | 42 | empty |
| 2 | 465 | 0.76 | 0.85 | 51 | empty |
| 3 | 440 | 0.76 | 0.85 | 49 | empty |
| 4 | 449 | 0.75 | 0.85 | 52 | empty |
| 5 | 396 | 0.75 | 0.85 | 53 | empty |
Interfaces
24 interfaces between chains.
- A–B · 2947 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 2929 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 2917 Ų buried · 18 hydrogen bonds · protein-protein
- K–M · 1998 Ų buried · 20 hydrogen bonds · protein-protein
- H–L · 1992 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 disulfide, 45 glycan (disulfide, N-glycosylation).
Compared structures
- 7LL2 · 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 7LL2 · PDBe 7LL2 · UniProt Q2N0S6 · UniProt Q2N0S7
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