Research workbench
Crystal structure of a humanized Fab (HU3S193) in complex with the lewis Y tetrasaccharide
Analyse Crystal structure of a humanized Fab (HU3S193) in complex with the lewis Y… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S3K
- Type
- protein
- Length
- 428 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HU3S193 Fab fragment, light chain; HU3S193 Fab fragment, heavy chain
- Ligands
- FUC, NDG, GAL
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | HU3S193 Fab fragment, light chain | protein | 216 | 5% helix, 51% strand | — |
| H | HU3S193 Fab fragment, heavy chain | protein | 212 | 8% helix, 55% strand | — |
Ligands and binding sites
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains L, H
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains H
- GAL · beta-D-galactopyranose · sugar · chains L, H
- GOL · Glycerol · additive · 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 | 591 | 0.64 | 0.75 | 62 | empty |
| 2 | 63 | 0.58 | 0.90 | 20 | empty |
| 3 | 116 | 0.41 | 0.75 | 19 | NDG, GAL, FUC |
| 4 | 53 | 0.29 | 0.75 | 12 | empty |
| 5 | 54 | 0.27 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- L–H · 1714 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1S3K · Crystal Structure of a Humanized Fab (hu3S193) in Complex with the Lewis Y Tetrasaccharide · the same entry in another collection · chain L against L, 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 1S3K · PDBe 1S3K
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