Research workbench
Three-dimensional structure of a fluorescein-Fab complex crystallized in 2-methyl-2,4-pentanediol
Analyse Three-dimensional structure of a fluorescein-Fab complex crystallized in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FAB
- Type
- protein
- Length
- 435 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG2A-kappa 4-4-20 Fab (light chain); IGG2A-kappa 4-4-20 Fab (heavy chain)
- UniProt
- P01865
- Ligands
- FLU
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | IGG2A-kappa 4-4-20 Fab (light chain) | protein | 219 | 5% helix, 45% strand | — |
| H | IGG2A-kappa 4-4-20 Fab (heavy chain) | protein | 216 | 11% helix, 38% strand | P01865 |
Ligands and binding sites
- FLU · 2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)-benzoic acid · ligand · chains L, H
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.56 | 0.75 | 55 | empty |
| 2 | 184 | 0.52 | 0.78 | 20 | FLU |
| 3 | 83 | 0.35 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- L–H · 1815 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4FAB · Three-dimensional structure of a fluorescein-Fab complex crystallized in… · the same entry in another collection · chain L against L, TM-score 1.00
- P01865 · AlphaFold monomer V2.0 prediction for ig gamma-2A chain C region, membrane-bound form… · a predicted model of the same protein · chain H against A, TM-score 0.47
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 P01865
- Elsewhere: RCSB PDB 4FAB · PDBe 4FAB · UniProt P01865
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