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Crystal structure of a monoclonal Fab specific for shigella flexneri Y lipopolysaccharide

Analyse Crystal structure of a monoclonal Fab specific for shigella flexneri Y… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1M71
Type: protein
Length: 435 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Light chain of the monoclonal antibody Fab SYA/J6; Heavy chain of the monoclonal antibody…
Pockets: 6 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Light chain of the monoclonal antibody Fab SYA/J6	protein	215	7% helix, 50% strand	—
B	Heavy chain of the monoclonal antibody Fab SYA/J6	protein	220	5% helix, 40% 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	561	0.60	0.73	60	empty
2	119	0.52	0.82	24	empty
3	107	0.50	0.81	21	empty
4	133	0.47	0.78	20	empty
5	120	0.41	0.75	23	empty

Interfaces

1 interface between chains.

A–B · 1666 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1M71 · Crystal structure of a Monoclonal Fab Specific for Shigella Flexneri Y lipopolysaccharide · the same entry in another collection · chain A against A, 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 1M71 · PDBe 1M71

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