Research workbench
Anti-lewis Y Fab fragment with lewis Y antigen in the presence of zinc ions
Analyse Anti-lewis Y Fab fragment with lewis Y antigen in the presence of zinc ions in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EYV
- Type
- protein
- Length
- 876 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HU3S193 Fab, light chain; HU3S193 Fab, heavy chain
- Ligands
- FUC, NDG, GAL, ZN
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | HU3S193 Fab, light chain | protein | 216 | 5% helix, 50% strand | — |
| H | HU3S193 Fab, heavy chain | protein | 219 | 5% helix, 49% strand | — |
| A | HU3S193 Fab, light chain | protein | 219 | 5% helix, 50% strand | — |
| B | HU3S193 Fab, heavy chain | protein | 222 | 5% helix, 51% 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
- ZN · Zinc ion · metal · 4 copies · chains L, H, B, A
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.77 | 0.80 | 105 | empty |
| 2 | 833 | 0.77 | 0.81 | 103 | empty |
| 3 | 61 | 0.56 | 0.89 | 23 | empty |
| 4 | 101 | 0.48 | 0.80 | 26 | empty |
| 5 | 68 | 0.45 | 0.83 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2029 Ų buried · 20 hydrogen bonds · protein-protein
- L–H · 1909 Ų buried · 21 hydrogen bonds · protein-protein
- H–B · 1059 Ų buried · 16 hydrogen bonds · protein-protein
- L–A · 302 Ų buried · 2 hydrogen bonds · protein-protein
- L–B · 95 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 3EYV · Anti-Lewis Y Fab fragment with Lewis Y antigen in the presence of zinc ions · 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 3EYV · PDBe 3EYV
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