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Structure of the heparin-induced E1-dimer of the amyloid precursor protein (app)

Analyse Structure of the heparin-induced E1-dimer of the amyloid precursor protein (app) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3KTM
Type: protein
Length: 1,396 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Amyloid beta A4 protein
UniProt: P05067
Ligands: BU4, SO4
Pockets: 18 · best druggability 0.79

Structure

x-ray diffraction · 7 distinct chains · 14% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	Amyloid beta A4 protein	protein	175	14% helix, 36% strand	P05067
B	Amyloid beta A4 protein	protein	173	14% helix, 33% strand	P05067
C	Amyloid beta A4 protein	protein	174	14% helix, 36% strand	P05067
D	Amyloid beta A4 protein	protein	173	14% helix, 35% strand	P05067
E	Amyloid beta A4 protein	protein	177	14% helix, 34% strand	P05067
G	Amyloid beta A4 protein	protein	174	14% helix, 36% strand	P05067
H	Amyloid beta A4 protein	protein	175	14% helix, 35% strand	P05067

Ligands and binding sites

BU4 · (3R)-butane-1,3-diol · ligand · 8 copies · chains A, B, C, D, E, F, G, H
SO4 · Sulfate ion · ion · 5 copies · chains B, C, D, E, H
ACT · Acetate ion · additive · 4 copies · chains B, C, E, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	430	0.79	0.87	54	empty
2	392	0.77	0.87	48	empty
3	459	0.77	0.85	59	empty
4	934	0.74	0.77	107	SO4
5	785	0.73	0.78	86	SO4

Interfaces

8 interfaces between chains.

G–H · 1345 Å² buried · 14 hydrogen bonds · protein-protein
A–E · 1327 Å² buried · 12 hydrogen bonds · protein-protein
C–F · 1297 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 703 Å² buried · 9 hydrogen bonds · protein-protein
F–H · 697 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 48 disulfide (disulfide).

Compared structures

3KTM · Structure of the Heparin-induced E1-Dimer of the Amyloid Precursor Protein (APP) · 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 D against A, TM-score 0.94

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 3KTM · PDBe 3KTM · UniProt P05067

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