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Alpha Synuclein fibril formed by full length protein - Rod Polymorph

Analyse Alpha Synuclein fibril formed by full length protein - Rod Polymorph in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6CU7
Type: protein
Length: 600 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.5
Source: Homo sapiens
Molecule: Alpha-synuclein
UniProt: P37840
Pockets: 6 · best druggability 0.75

Structure

electron microscopy · resolution 3.5 · 1 distinct chain · 0% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, A, B, C, D, F, G, H, I, J	Alpha-synuclein	protein	60	0% helix, 55% strand	P37840

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	632	0.75	0.82	48	empty
2	602	0.73	0.81	47	empty
3	320	0.59	0.77	28	empty
4	301	0.55	0.76	27	empty
5	63	0.29	0.74	17	empty

Interfaces

25 interfaces between chains.

G–I · 2446 Å² buried · 77 hydrogen bonds · protein-protein
E–C · 2431 Å² buried · 72 hydrogen bonds · protein-protein
F–H · 2427 Å² buried · 74 hydrogen bonds · protein-protein
D–F · 2425 Å² buried · 70 hydrogen bonds · protein-protein
H–J · 2415 Å² buried · 68 hydrogen bonds · protein-protein

Compared structures

6CU7 · Alpha synuclein fibril formed by full length protein - rod polymorph · the same entry in another collection · chain J against J, TM-score 1.00
P37840 · AlphaFold monomer V2.0 prediction for alpha-synuclein (P37840) · a predicted model of the same protein · chain E against A, TM-score 0.28

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 P37840
Elsewhere: RCSB PDB 6CU7 · PDBe 6CU7 · UniProt P37840

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