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Structure of the tethered N-terminus of ALZHEIMER'S disease a peptide

Analyse Structure of the tethered N-terminus of ALZHEIMER'S disease a peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4F37
Type: protein
Length: 1,090 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Colicin-E7 immunity protein; IM7 immunity protein; Fab WO2 anti-amyloid-beta antibody Fab…
UniProt: Q03708
Pockets: 17 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 10% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Colicin-E7 immunity protein	protein	102	43% helix, 0% strand	Q03708
F, H	IM7 immunity protein	protein	225	3% helix, 32% strand	—
K, L	Fab WO2 anti-amyloid-beta antibody Fab fragment	protein	218	2% helix, 29% strand	—

Pockets

17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	618	0.74	0.81	67	empty
2	50	0.69	0.97	16	empty
3	619	0.66	0.76	72	empty
4	396	0.57	0.75	54	empty
5	217	0.57	0.79	32	empty

Interfaces

9 interfaces between chains.

H–L · 2041 Å² buried · 16 hydrogen bonds · protein-protein
F–K · 1914 Å² buried · 14 hydrogen bonds · protein-protein
A–H · 483 Å² buried · 8 hydrogen bonds · protein-protein
B–F · 472 Å² buried · 5 hydrogen bonds · protein-protein
B–L · 463 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

4F37 · Structure of the tethered N-terminus of Alzheimer's disease A peptide · the same entry in another collection · chain F against F, TM-score 1.00
Q03708 · AlphaFold monomer V2.0 prediction for colicin-E7 immunity protein (Q03708) · a predicted model of the same protein · chain A against A, TM-score 0.78

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 Q03708
Elsewhere: RCSB PDB 4F37 · PDBe 4F37 · UniProt Q03708

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