Research workbench

PFA2 FAB complexed with Abeta1-8

Analyse PFA2 FAB complexed with Abeta1-8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2R0W
Type: protein
Length: 443 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.503
Source: Mus musculus; SYNTHETIC CONSTRUCT
Molecule: IgG2a Fab fragment light chain; IgG2a Fab fragment heavy chain, Fd portion; Amyloid beta…
UniProt: A2NHM3, Q811U5, P05067
Ligands: NA
Pockets: 4 · best druggability 0.51

Structure

x-ray diffraction · resolution 2.503 · 3 distinct chains · 6% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	IgG2a Fab fragment light chain	protein	219	7% helix, 51% strand	A2NHM3
H	IgG2a Fab fragment heavy chain, Fd portion	protein	217	6% helix, 49% strand	Q811U5
Q	Amyloid beta peptide fragment	protein	7	0% helix, 14% strand	P05067

Ligands and binding sites

NA · Sodium ion · metal · chains 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	257	0.51	0.75	40	empty
2	137	0.41	0.74	25	empty
3	64	0.31	0.75	18	empty
4	59	0.27	0.73	16	empty

Interfaces

3 interfaces between chains.

L–H · 1845 Å² buried · 17 hydrogen bonds · protein-protein
L–Q · 362 Å² buried · 10 hydrogen bonds · protein-protein
H–Q · 344 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 1 modified (disulfide, alkylation).

Compared structures

2R0W · PFA2 Fab complexed with ABETA1-8 · 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 Q against A, TM-score 0.57

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 A2NHM3
Every structure of UniProt Q811U5
Every structure of UniProt P05067
Elsewhere: RCSB PDB 2R0W · PDBe 2R0W · UniProt A2NHM3 · UniProt Q811U5 · UniProt P05067

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.