MolNFT v1 · #55426 · protein

Structure of human anti-nicotine Fab fragment in complex with nicotine

2YK1 · Fab fragment, heavy chain: “Structure of human anti-nicotine Fab fragment in complex with nicotine”. X-ray diffraction, 1 ligand (NCT), 3 pockets (best druggability 0.72). MolNFT v1 #55426 on GenesisL1: 3D structure, binding sites…

PDB: 2YK1
Type: protein
Length: 370 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: NCT
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 3% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab fragment, heavy chain	protein	182	5% helix, 52% strand	—
L	Fab fragment, light chain	protein	188	2% helix, 52% strand	—

Ligands and binding sites

NCT · (S)-3-(1-methylpyrrolidin-2-yl)pyridine · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	65	0.72	0.97	18	NCT
2	282	0.49	0.73	40	empty
3	93	0.38	0.76	21	empty

Interfaces

1 interface between chains.

H–L · 1536 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

2YK1 · Structure of human anti-nicotine Fab fragment in complex with nicotine · 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 2YK1 · PDBe 2YK1

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