MolNFT v1 · #28445 · protein
Structure of IGG2A Fab fragment
1YEH: “Structure of IGG2A Fab fragment”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.62). MolNFT v1 #28445 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1YEH
- Type
- protein
- Length
- 441 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab fragment
- UniProt
- P01863
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab fragment | protein | 219 | 5% helix, 53% strand | — |
| H | Fab fragment | protein | 222 | 7% helix, 52% strand | P01863 |
Ligands and binding sites
- ZN · Zinc ion · metal · 7 copies · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.62 | 0.84 | 24 | empty |
| 2 | 200 | 0.43 | 0.73 | 36 | empty |
| 3 | 55 | 0.36 | 0.79 | 14 | empty |
| 4 | 61 | 0.27 | 0.73 | 21 | empty |
| 5 | 54 | 0.27 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- L–H · 2080 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
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 P01863
- Elsewhere: RCSB PDB 1YEH · PDBe 1YEH · UniProt P01863
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