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Crystal structure of the Fab fragment of humanized 5C8 antibody containing the fluorescent non-canonical amino acid L-(7- hydroxycoumarin-4-YL)ETHYLGLYCINE at pH 9.7

Analyse Crystal structure of the Fab fragment of humanized 5C8 antibody containing the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6W5A
Type: protein
Length: 434 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antibody 5C8* Fab heavy chain; Antibody 5C8* Fab light chain
Pockets: 3 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Antibody 5C8* Fab heavy chain	protein	219	11% helix, 51% strand	—
L	Antibody 5C8* Fab light chain	protein	215	6% helix, 51% strand	—

Pockets

3 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	617	0.63	0.74	68	empty
2	61	0.53	0.88	20	empty
3	79	0.32	0.73	22	empty

Interfaces

1 interface between chains.

H–L · 1789 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 2 modified (disulfide, cyclization, nonstandard).

Compared structures

6W5A · Crystal Structure of the Fab fragment of humanized 5c8 antibody containing the… · 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 6W5A · PDBe 6W5A

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