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Crystal structure of the therapeutical antibody fragment of canakinumab in its unbound state

Analyse Crystal structure of the therapeutical antibody fragment of canakinumab in its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4G5Z
Type: protein
Length: 430 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Canakinumab antibody fragment heavy chain; Canakinumab antibody fragment light chain
Pockets: 5 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Canakinumab antibody fragment heavy chain	protein	218	10% helix, 53% strand	—
L	Canakinumab antibody fragment light chain	protein	212	6% helix, 51% strand	—

Pockets

5 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	447	0.63	0.77	58	empty
2	54	0.53	0.89	21	empty
3	85	0.36	0.76	22	empty
4	80	0.33	0.74	19	empty
5	62	0.31	0.75	19	empty

Interfaces

1 interface between chains.

H–L · 1866 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4G5Z · Crystal structure of the therapeutical antibody fragment of canakinumab in its unbound… · 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 4G5Z · PDBe 4G5Z

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