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Structure of human anti-nicotine Fab fragment in complex with nicotine-11-yl-methyl-(4-ethylamino-4-oxo)-butanoate

Analyse Structure of human anti-nicotine Fab fragment in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2YKL
Type: protein
Length: 381 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab fragment, heavy chain; Fab fragment, light chain
Ligands: NLD
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab fragment, heavy chain	protein	181	5% helix, 52% strand	—
L	Fab fragment, light chain	protein	200	4% helix, 51% strand	—

Ligands and binding sites

NLD · Nicotine-11-yl-methyl-(4-ethylamino-4-oxo)-butanoate · ligand · chains H, L

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

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	97	0.72	0.94	19	NLD
2	349	0.52	0.73	44	empty
3	61	0.28	0.74	17	empty

Interfaces

1 interface between chains.

H–L · 1489 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

2YKL · Structure of human anti-nicotine Fab fragment in complex with… · 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 2YKL · PDBe 2YKL

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