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Fab fragment of chikungunya virus neutralizing human monoclonal antibody 4J21

Analyse Fab fragment of chikungunya virus neutralizing human monoclonal antibody 4J21 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5CGY
Type: protein
Length: 869 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heavy chain of Fab; Light chain of Fab
Pockets: 7 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, C	Heavy chain of Fab	protein	222	11% helix, 49% strand	—
L	Light chain of Fab	protein	213	6% helix, 52% strand	—
D	Light chain of Fab	protein	212	6% helix, 54% strand	—

Pockets

7 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	624	0.63	0.74	61	empty
2	610	0.63	0.74	58	empty
3	248	0.51	0.75	48	empty
4	92	0.38	0.77	19	empty
5	54	0.38	0.80	15	empty

Interfaces

3 interfaces between chains.

H–L · 1734 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 1693 Å² buried · 9 hydrogen bonds · protein-protein
H–C · 250 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 5CGY · PDBe 5CGY

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