Research workbench

S8 phosphorylated beta amyloid 40 fibrils

Analyse S8 phosphorylated beta amyloid 40 fibrils in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6OC9
Type: protein
Length: 400 residues
Chains: 10
Method: solid-state nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Amyloid-beta precursor protein
UniProt: P05067
Ligands: 2PO
Pockets: 9 · best druggability 0.72

Structure

solid-state nmr · 1 distinct chain · 0% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J	Amyloid-beta precursor protein	protein	40	0% helix, 33% strand	P05067

Ligands and binding sites

2PO · Phosphonate · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J

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

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	292	0.72	0.85	40	empty
2	137	0.67	0.89	29	empty
3	295	0.64	0.81	45	empty
4	77	0.64	0.92	29	2PO
5	208	0.62	0.82	38	empty

Interfaces

25 interfaces between chains.

G–H · 1602 Å² buried · 44 hydrogen bonds · protein-protein
I–J · 1573 Å² buried · 41 hydrogen bonds · protein-protein
D–E · 1568 Å² buried · 46 hydrogen bonds · protein-protein
B–C · 1562 Å² buried · 42 hydrogen bonds · protein-protein
H–I · 1470 Å² buried · 35 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 covalent (covalent ligand).

Compared structures

6OC9 · S8 phosphorylated beta amyloid 40 fibrils · the same entry in another collection · chain C against C, TM-score 1.00
P05067 · AlphaFold monomer V2.0 prediction for amyloid-beta precursor protein (P05067) · a predicted model of the same protein · chain C against A, TM-score 0.38

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 6OC9 · PDBe 6OC9 · UniProt P05067

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