MolNFT v1 · #55519 · protein

Crystal structure of inhibitory anti-ache FAB408

2YMX · Fab antibody heavy chain: “Crystal structure of inhibitory anti-ache FAB408”. X-ray diffraction, 4 pockets (best druggability 0.63). MolNFT v1 #55519 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2YMX
Type: protein
Length: 435 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab antibody heavy chain; Fab antibody light chain
Pockets: 4 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab antibody heavy chain	protein	222	8% helix, 51% strand	—
L	Fab antibody light chain	protein	213	6% helix, 51% strand	—

Ligands and binding sites

GOL · Glycerol · additive · chains H, L

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

Pockets

4 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	616	0.63	0.75	69	empty
2	214	0.48	0.74	39	empty
3	81	0.31	0.73	22	empty
4	50	0.27	0.75	12	empty

Interfaces

1 interface between chains.

H–L · 1851 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

2YMX · Crystal structure of inhibitory anti-AChE Fab408 · 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 2YMX · PDBe 2YMX

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