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Crystal structure of Fab fragment of anti-mesothelin antibody

Analyse Crystal structure of Fab fragment of anti-mesothelin antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7VSU
Type: protein
Length: 877 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Light chain; Heavy chain
Pockets: 9 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, A	Light chain	protein	212	6% helix, 50% strand	—
D	Heavy chain	protein	230	7% helix, 49% strand	—
B	Heavy chain	protein	223	7% helix, 51% strand	—

Pockets

9 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	725	0.66	0.75	56	empty
2	693	0.65	0.75	54	empty
3	213	0.54	0.78	31	empty
4	68	0.50	0.85	21	empty
5	67	0.48	0.85	21	empty

Interfaces

2 interfaces between chains.

A–B · 2048 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 2031 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

7VSU · Crystal structure of Fab fragment of anti-mesothelin antibody · the same entry in another collection · chain C against C, 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 7VSU · PDBe 7VSU

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