MolNFT v1 · #49846 · protein

PFA2 Fab complexed with ABETA1-8

2R0W · IGG2A Fab fragment light chain: “PFA2 Fab complexed with ABETA1-8”. X-ray diffraction, 1 ligand (NA), 4 pockets (best druggability 0.51). MolNFT v1 #49846 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2R0W
Type: protein
Length: 443 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
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 · 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 L against L, 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

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