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Crystal structure of anti-mouse CD3EPSILON antibody 2C11 Fab fragment

Analyse Crystal structure of anti-mouse CD3EPSILON antibody 2C11 Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3R06
Type: protein
Length: 1,695 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Anti-mouse CD3EPSILON antibody 2C11 Fab light chain; Anti-mouse CD3EPSILON antibody 2C11…
Pockets: 20 · best druggability 0.65

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, L	Anti-mouse CD3EPSILON antibody 2C11 Fab light chain	protein	213	6% helix, 52% strand	—
B	Anti-mouse CD3EPSILON antibody 2C11 Fab heavy chain	protein	210	7% helix, 53% strand	—
D, F, H	Anti-mouse CD3EPSILON antibody 2C11 Fab heavy chain	protein	211	7% helix, 54% strand	—

Pockets

20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	495	0.65	0.77	38	empty
2	479	0.58	0.74	46	empty
3	316	0.55	0.76	36	empty
4	229	0.54	0.77	37	empty
5	210	0.53	0.78	27	empty

Interfaces

9 interfaces between chains.

E–F · 1840 Å² buried · 15 hydrogen bonds · protein-protein
H–L · 1798 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1794 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 1785 Å² buried · 16 hydrogen bonds · protein-protein
C–H · 289 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

3R06 · Crystal structure of anti-mouse CD3epsilon antibody 2C11 Fab fragment · 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 3R06 · PDBe 3R06

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