Research workbench
Anti-lewis X Fab fragment in complex with lewis X
Analyse Anti-lewis X Fab fragment in complex with lewis X in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UZ8
- Type
- protein
- Length
- 860 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IgG Fab (IGG3, kappa) light chain 291-2G3-a; IgG Fab (IGG3, kappa) heavy chain 291-2G3-a
- Ligands
- MAG, FUC, GAL
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | IgG Fab (IGG3, kappa) light chain 291-2G3-a | protein | 218 | 6% helix, 47% strand | — |
| B, H | IgG Fab (IGG3, kappa) heavy chain 291-2G3-a | protein | 212 | 8% helix, 52% strand | — |
Ligands and binding sites
- MAG · methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside · sugar · 2 copies · chains A, B, L, H
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B, H, L
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B, L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 805 | 0.67 | 0.74 | 73 | empty |
| 2 | 777 | 0.66 | 0.74 | 74 | empty |
| 3 | 531 | 0.66 | 0.77 | 43 | MAG, FUC, GAL |
| 4 | 97 | 0.54 | 0.84 | 22 | empty |
| 5 | 120 | 0.44 | 0.77 | 29 | empty |
Interfaces
5 interfaces between chains.
- H–L · 1768 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1763 Ų buried · 24 hydrogen bonds · protein-protein
- A–L · 106 Ų buried · 0 hydrogen bonds · protein-protein
- B–L · 106 Ų buried · 1 hydrogen bond · protein-protein
- A–H · 103 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1UZ8 · anti-Lewis X Fab fragment in complex with Lewis X · the same entry in another collection · chain A against A, 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 1UZ8 · PDBe 1UZ8
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