Research workbench

PFA1 Fab fragment complexed with abeta 1-8 peptide

Analyse PFA1 Fab fragment complexed with abeta 1-8 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2IPU
Type: protein
Length: 894 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: IGG2A Fab fragment heavy chain; IGG2A Fab fragment light chain kappa; Abeta 1-8 peptide
Ligands: ACM
Pockets: 8 · best druggability 0.57

Structure

x-ray diffraction · 4 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, K	IGG2A Fab fragment heavy chain	protein	219	8% helix, 51% strand	—
H	IGG2A Fab fragment light chain kappa	protein	223	7% helix, 48% strand	—
G	IGG2A Fab fragment light chain kappa	protein	219	7% helix, 51% strand	—
P, Q	Abeta 1-8 peptide	protein	7	0% helix, 14% strand	—

Ligands and binding sites

ACM · Acetamide · ligand · 3 copies · chains L, H, K, G
GOL · Glycerol · additive · 6 copies · chains L, H, K

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	402	0.57	0.75	55	empty
2	340	0.55	0.75	34	empty
3	297	0.53	0.75	41	empty
4	73	0.34	0.75	19	GOL
5	80	0.33	0.74	20	empty

Interfaces

7 interfaces between chains.

L–H · 1892 Å² buried · 19 hydrogen bonds · protein-protein
K–G · 1841 Å² buried · 20 hydrogen bonds · protein-protein
L–Q · 367 Å² buried · 9 hydrogen bonds · protein-protein
K–P · 359 Å² buried · 8 hydrogen bonds · protein-protein
G–P · 334 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 3 covalent (disulfide, covalent ligand).

Compared structures

2IPU · PFA1 Fab fragment complexed with Abeta 1-8 peptide · the same entry in another collection · chain L against L, 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 2IPU · PDBe 2IPU

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