MolNFT v1 · #102488 · protein

Fab fragment of 3D6 in complex with amyloid beta 1-40

4ONG · 3D6 Fab antibody heavy chain: “Fab fragment of 3D6 in complex with amyloid beta 1-40”. X-ray diffraction, 2 ligands (ZN, CL), 2 pockets (best druggability 0.64). MolNFT v1 #102488 on GenesisL1: 3D structure, binding sites and…

PDB: 4ONG
Type: protein
Length: 429 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3D6 Fab antibody heavy chain; 3D6 Fab antibody light chain; Amyloid beta A4 protein
UniProt: P05067
Ligands: ZN, CL
Pockets: 2 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	3D6 Fab antibody heavy chain	protein	210	9% helix, 53% strand	—
L	3D6 Fab antibody light chain	protein	214	6% helix, 53% strand	—
P	Amyloid beta A4 protein	protein	5	60% helix, 0% strand	P05067

Ligands and binding sites

ZN · Zinc ion · metal · 27 copies · chains H, L, P
CL · Chloride ion · ion · 11 copies · chains H, L
IMD · Imidazole · additive · 3 copies · chains H, L

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

Pockets

2 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	642	0.64	0.74	64	ZN, IMD, CL
2	141	0.43	0.76	28	ZN

Interfaces

3 interfaces between chains.

H–L · 1779 Å² buried · 17 hydrogen bonds · protein-protein
H–P · 328 Å² buried · 7 hydrogen bonds · protein-protein
L–P · 303 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4ONG · Fab fragment of 3D6 in complex with amyloid beta 1-40 · the same entry in another collection · chain H against H, TM-score 1.00
P05067 · AlphaFold monomer V2.0 prediction for amyloid-beta precursor protein (P05067) · a predicted model of the same protein · chain P against A, TM-score 0.81

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P05067
Elsewhere: RCSB PDB 4ONG · PDBe 4ONG · UniProt P05067

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