Research workbench
Crystal structure of a recombinant IgE Fab fragment in complex with bovine beta-lactoglobulin allergen
Analyse Crystal structure of a recombinant IgE Fab fragment in complex with bovine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R56
- Type
- protein
- Length
- 1,182 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactoglobulin; IgE Fab fragment, light chain; IgE Fab fragment, heavy chain
- UniProt
- P02754
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactoglobulin | protein | 159 | 16% helix, 42% strand | P02754 |
| L, M | IgE Fab fragment, light chain | protein | 211 | 5% helix, 52% strand | — |
| H, I | IgE Fab fragment, heavy chain | protein | 221 | 5% helix, 50% strand | — |
Ligands and binding sites
- LMT · Dodecyl-beta-D-maltoside · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.73 | 0.88 | 28 | LMT |
| 2 | 194 | 0.72 | 0.87 | 26 | LMT |
| 3 | 661 | 0.64 | 0.74 | 53 | empty |
| 4 | 290 | 0.60 | 0.78 | 39 | empty |
| 5 | 526 | 0.59 | 0.73 | 61 | empty |
Interfaces
7 interfaces between chains.
- M–I · 1871 Ų buried · 10 hydrogen bonds · protein-protein
- L–H · 1866 Ų buried · 12 hydrogen bonds · protein-protein
- A–H · 579 Ų buried · 10 hydrogen bonds · protein-protein
- B–I · 565 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 552 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 2R56 · Crystal Structure of a Recombinant IgE Fab Fragment in Complex with Bovine… · the same entry in another collection · chain H against H, TM-score 1.00
- P02754 · AlphaFold monomer V2.0 prediction for beta-lactoglobulin (P02754) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P02754
- Elsewhere: RCSB PDB 2R56 · PDBe 2R56 · UniProt P02754
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