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Structure of the Fab fragment of ab-52, an antibody that binds the O- antigen of francisella tularensis

Analyse Structure of the Fab fragment of ab-52, an antibody that binds the O- antigen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3UJT
Type: protein
Length: 848 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ab-52 heavy chain; Ab-52 light chain
Pockets: 11 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, I	Ab-52 heavy chain	protein	207	9% helix, 54% strand	—
L, M	Ab-52 light chain	protein	217	6% helix, 53% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 4 copies · chains H, L, M
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains H, L, I, M

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	366	0.68	0.81	55	empty
2	622	0.65	0.75	64	empty
3	312	0.55	0.76	41	GOL
4	68	0.46	0.83	24	empty
5	129	0.41	0.75	25	empty

Interfaces

4 interfaces between chains.

I–M · 1706 Å² buried · 13 hydrogen bonds · protein-protein
H–L · 1611 Å² buried · 13 hydrogen bonds · protein-protein
H–M · 506 Å² buried · 6 hydrogen bonds · protein-protein
L–M · 268 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

3UJT · Structure of the Fab fragment of Ab-52, an antibody that binds the O-antigen of… · 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 3UJT · PDBe 3UJT

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