MolNFT v1 · #28440 · protein
Structure of a catalytic antibody IGG2A Fab fragment (D2.3)
1YEC: “Structure of a catalytic antibody IGG2A Fab fragment (D2.3)”. X-ray diffraction, 2 ligands (PNB, ZN), 4 pockets (best druggability 0.63). MolNFT v1 #28440 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1YEC
- Type
- protein
- Length
- 441 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG2A Fab fragment (D2.3)
- UniProt
- P01863
- Ligands
- PNB, ZN
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | IGG2A Fab fragment (D2.3) | protein | 219 | 5% helix, 53% strand | — |
| H | IGG2A Fab fragment (D2.3) | protein | 222 | 7% helix, 52% strand | P01863 |
Ligands and binding sites
- PNB · 4-nitro-benzylphosphonobutanoyl-glycine · ligand · chains L, H
- 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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.63 | 0.85 | 25 | PNB |
| 2 | 229 | 0.45 | 0.72 | 38 | empty |
| 3 | 64 | 0.34 | 0.77 | 15 | empty |
| 4 | 66 | 0.29 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- L–H · 2057 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1YEC · Structure of a catalytic antibody IGG2A Fab fragment (D2.3) · the same entry in another collection · chain L against L, TM-score 1.00
- P01863 · AlphaFold monomer V2.0 prediction for ig gamma-2A chain C region, a allele (P01863) · 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 P01863
- Elsewhere: RCSB PDB 1YEC · PDBe 1YEC · UniProt P01863
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