Research workbench
Structure of uncomplexed Fab compared to complex (1CLY, 1CLZ)
Analyse Structure of uncomplexed Fab compared to complex (1CLY, 1CLZ) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UCB
- Type
- protein
- Length
- 435 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimeric HUMAN/MOUSE IgG Fab fragment BR96
- UniProt
- P01834
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Chimeric HUMAN/MOUSE IgG Fab fragment BR96 | protein | 216 | 6% helix, 50% strand | P01834 |
| H | Chimeric HUMAN/MOUSE IgG Fab fragment BR96 | protein | 219 | 8% helix, 53% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.62 | 0.74 | 69 | empty |
| 2 | 60 | 0.60 | 0.92 | 19 | empty |
| 3 | 82 | 0.34 | 0.74 | 14 | empty |
| 4 | 72 | 0.32 | 0.74 | 17 | empty |
| 5 | 62 | 0.28 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- L–H · 1837 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1UCB · Structure of uncomplexed Fab compared to complex (1CLY, 1CLZ) · the same entry in another collection · chain L against L, TM-score 1.00
- P01834 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01834) · a predicted model of the same protein · chain L against A, TM-score 0.49
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 P01834
- Elsewhere: RCSB PDB 1UCB · PDBe 1UCB · UniProt P01834
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