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Crystal structure analysis of app E2 domain

Analyse Crystal structure analysis of app E2 domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3NYJ
Type: protein
Length: 181 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Amyloid beta A4 protein
UniProt: P05067
Ligands: OS
Pockets: 2 · best druggability 0.34

Structure

x-ray diffraction · 1 distinct chain · 83% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Amyloid beta A4 protein	protein	181	83% helix, 0% strand	P05067

Ligands and binding sites

OS · Osmium ion · metal · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	81	0.34	0.75	18	empty
2	64	0.32	0.76	16	empty

Modifications

Observed in the structure: 8 modified (engineered).

Compared structures

3NYJ · Crystal Structure Analysis of APP E2 domain · the same entry in another collection · chain A against A, TM-score 1.00
P05067 · AlphaFold monomer V2.0 prediction for amyloid-beta precursor protein (P05067) · a predicted model of the same protein · chain A against A, TM-score 0.90

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 3NYJ · PDBe 3NYJ · UniProt P05067

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