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Comparison of the three-dimensional structures of a humanized and a chimeric Fab of an anti-gamma-interferon antibody

Analyse Comparison of the three-dimensional structures of a humanized and a chimeric… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1B4J
Type: protein
Length: 434 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antibody
Pockets: 6 · best druggability 0.61

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Antibody	protein	214	5% helix, 42% strand	—
H	Antibody	protein	220	3% helix, 44% strand	—

Pockets

6 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	60	0.61	0.91	23	empty
2	210	0.52	0.77	28	empty
3	55	0.46	0.85	21	empty
4	180	0.44	0.74	35	empty
5	92	0.34	0.74	15	empty

Interfaces

1 interface between chains.

L–H · 1898 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 1 modified (disulfide, cyclization).

Compared structures

1B4J · Comparison of the three-dimensional structures of a humanized and a chimeric Fab of an… · the same entry in another collection · chain H against H, 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 1B4J · PDBe 1B4J

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