Research workbench
Structure of a catalytic antibody, IGG2A Fab fragment (D2.5)
Analyse Structure of a catalytic antibody, IGG2A Fab fragment (D2.5) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YEE
- Type
- protein
- Length
- 441 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG2A Fab fragment (D2.5)
- UniProt
- P01865
- Ligands
- PNB
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | IGG2A Fab fragment (D2.5) | protein | 219 | 5% helix, 51% strand | — |
| H | IGG2A Fab fragment (D2.5) | protein | 222 | 7% helix, 55% strand | P01865 |
Ligands and binding sites
- PNB · 4-nitro-benzylphosphonobutanoyl-glycine · ligand · 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 | 169 | 0.69 | 0.87 | 25 | PNB |
| 2 | 160 | 0.40 | 0.73 | 25 | empty |
| 3 | 50 | 0.30 | 0.76 | 19 | empty |
| 4 | 63 | 0.29 | 0.74 | 16 | empty |
| 5 | 53 | 0.27 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- L–H · 2066 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1YEE · Structure of a catalytic antibody, IGG2A Fab fragment (D2.5) · the same entry in another collection · chain L against L, TM-score 1.00
- P01865 · AlphaFold monomer V2.0 prediction for ig gamma-2A chain C region, membrane-bound form… · a predicted model of the same protein · chain H against A, TM-score 0.50
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 P01865
- Elsewhere: RCSB PDB 1YEE · PDBe 1YEE · UniProt P01865
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