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Catalytic antibody 28B4 Fab fragment

Analyse Catalytic antibody 28B4 Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1KEM
Type: protein
Length: 435 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 28B4 Fab
UniProt: P01868
Pockets: 2 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	28B4 Fab	protein	217	6% helix, 50% strand	—
H	28B4 Fab	protein	218	6% helix, 52% strand	P01868

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	425	0.56	0.74	54	empty
2	85	0.54	0.85	17	empty

Interfaces

1 interface between chains.

L–H · 1786 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1KEM · Catalytic antibody 28B4 Fab fragment · the same entry in another collection · chain L against L, TM-score 1.00
P01868 · AlphaFold monomer V2.0 prediction for ig gamma-1 chain C region secreted form (P01868) · a predicted model of the same protein · chain H against A, TM-score 0.48

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 P01868
Elsewhere: RCSB PDB 1KEM · PDBe 1KEM · UniProt P01868

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