MolNFT v1 · #113379 · protein

Crystal structure of the paraoxon-modified A.17 antibody Fab fragment - light chain S35R mutant

5ADO · Fab A.17: “Crystal structure of the paraoxon-modified A.17 antibody Fab fragment - light chain S35R mutant”. X-ray diffraction, 1 ligand (DEP), 4 pockets (best druggability 0.61). MolNFT v1 #113379 on GenesisL1: 3D structure…

PDB: 5ADO
Type: protein
Length: 424 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab A.17
Ligands: DEP
Pockets: 4 · best druggability 0.61

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab A.17	protein	211	9% helix, 52% strand	—
L	Fab A.17	protein	213	6% helix, 49% strand	—

Ligands and binding sites

DEP · Diethyl phosphonate · ligand · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	515	0.61	0.75	52	empty
2	117	0.60	0.85	27	DEP
3	86	0.40	0.78	23	empty
4	65	0.33	0.76	18	empty

Interfaces

1 interface between chains.

H–L · 1668 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

5ADO · Crystal structure of the paraoxon-modified A.17 antibody FAB fragment - Light chain S35R… · 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 5ADO · PDBe 5ADO

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