Research workbench
Cryo-EM structure of Q23.17_DS-sosip in complex with GLYCAN276- dependent broadly neutralizing antibody 179NC75 Fab
Analyse Cryo-EM structure of Q23.17_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
- 7LLK
- Type
- protein
- Length
- 2,397 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120; Envelope glycoprotein GP41; 179NC75 Fab heavy chain; 179NC75…
- UniProt
- O55774
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 18% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, A, I | Envelope glycoprotein GP120 | protein | 440 | 13% helix, 36% strand | O55774 |
| F, B, J | Envelope glycoprotein GP41 | protein | 126 | 57% helix, 2% strand | — |
| G, C, K | 179NC75 Fab heavy chain | protein | 131 | 8% helix, 30% strand | — |
| H, D, L | 179NC75 Fab light chain | protein | 102 | 0% helix, 41% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 74 copies · chains E, F, I, J, H, G, A, D, C, L, K, B
- BMA · beta-D-mannopyranose · sugar · 28 copies · chains K, G, D, C, L
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains G, C, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.84 | 0.86 | 116 | empty |
| 2 | 345 | 0.75 | 0.86 | 45 | empty |
| 3 | 386 | 0.72 | 0.84 | 50 | empty |
| 4 | 76 | 0.71 | 0.96 | 23 | empty |
| 5 | 140 | 0.64 | 0.87 | 35 | empty |
Interfaces
24 interfaces between chains.
- E–F · 2727 Ų buried · 19 hydrogen bonds · protein-protein
- I–J · 2699 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2672 Ų buried · 21 hydrogen bonds · protein-protein
- B–J · 1188 Ų buried · 9 hydrogen bonds · protein-protein
- F–B · 1173 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide, 36 glycan (disulfide, N-glycosylation).
Compared structures
- 7LLK · Cryo-EM structure of Q23.17_DS-SOSIP in complex with Glycan276-Dependent Broadly… · the same entry in another collection · chain E against E, 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 O55774
- Elsewhere: RCSB PDB 7LLK · PDBe 7LLK · UniProt O55774
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