Research workbench
A non-self sugar mimic of the HIV glycan shield shows enhanced antigenicity
Analyse A non-self sugar mimic of the HIV glycan shield shows enhanced antigenicity in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OB0
- Type
- protein
- Length
- 864 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.85
- Source
- Homo sapiens
- Molecule
- Fab 2G12, light chain; Fab 2G12, heavy chain
- Ligands
- MAN, YYH
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.85 · 4 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab 2G12, light chain | protein | 212 | 6% helix, 53% strand | — |
| H | Fab 2G12, heavy chain | protein | 220 | 7% helix, 51% strand | — |
| K | Fab 2G12, light chain | protein | 213 | 6% helix, 53% strand | — |
| M | Fab 2G12, heavy chain | protein | 219 | 4% helix, 52% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains H, L, M, K
- YYH · 7-deoxy-L-glycero-alpha-D-manno-heptopyranose · sugar · 2 copies · chains L, H, K, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.75 | 0.78 | 97 | empty |
| 2 | 546 | 0.64 | 0.76 | 52 | empty |
| 3 | 426 | 0.64 | 0.78 | 46 | empty |
| 4 | 119 | 0.37 | 0.74 | 25 | empty |
| 5 | 97 | 0.36 | 0.75 | 19 | empty |
Interfaces
6 interfaces between chains.
- H–M · 988 Ų buried · 15 hydrogen bonds · protein-protein
- L–H · 967 Ų buried · 10 hydrogen bonds · protein-protein
- K–M · 954 Ų buried · 12 hydrogen bonds · protein-protein
- H–K · 952 Ų buried · 8 hydrogen bonds · protein-protein
- L–M · 911 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3OB0 · A non-self sugar mimic of the HIV glycan shield shows enhanced antigenicity · the same entry in another collection · chain H against H, 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
- Elsewhere: RCSB PDB 3OB0 · PDBe 3OB0
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