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Crystal structure of an anti-carbohydrate antibody directed against vibrio cholerae O1 in complex with antigen

Analyse Crystal structure of an anti-carbohydrate antibody directed against vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1F4W
Type: protein
Length: 426 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antibody S-20-4, Fab fragment, light chain; Antibody S-20-4, Fab fragment, heavy chain
Pockets: 4 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Antibody S-20-4, Fab fragment, light chain	protein	210	8% helix, 55% strand	—
H	Antibody S-20-4, Fab fragment, heavy chain	protein	216	7% helix, 52% strand	—

Pockets

4 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	532	0.65	0.77	62	empty
2	213	0.53	0.78	34	empty
3	76	0.31	0.73	13	empty
4	50	0.26	0.74	17	empty

Interfaces

1 interface between chains.

L–H · 1813 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1F4W · Crystal structure of an anti-carbohydrate antibody directed against vibrio cholerae O1 in… · the same entry in another collection · chain L against L, 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 1F4W · PDBe 1F4W

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