MolNFT v1 · #163109 · protein

Cryo-EM structure of alpha-synuclein fibril polymorph 2A

6RT0: “Cryo-EM structure of alpha-synuclein fibril polymorph 2A”. Electron microscopy, 8 pockets (best druggability 0.64). MolNFT v1 #163109 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6RT0
Type: protein
Length: 735 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-synuclein
UniProt: P37840
Pockets: 8 · best druggability 0.64

Structure

electron microscopy · 2 distinct chains · 0% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Alpha-synuclein	protein	74	0% helix, 53% strand	P37840
F, G, H, I, J	Alpha-synuclein	protein	73	0% helix, 52% strand	P37840

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	119	0.64	0.89	47	empty
2	110	0.62	0.88	48	empty
3	108	0.38	0.75	23	empty
4	82	0.34	0.75	23	empty
5	92	0.33	0.73	15	empty

Interfaces

19 interfaces between chains.

B–C · 2899 Å² buried · 88 hydrogen bonds · protein-protein
F–H · 2855 Å² buried · 82 hydrogen bonds · protein-protein
D–E · 2838 Å² buried · 82 hydrogen bonds · protein-protein
A–B · 2833 Å² buried · 82 hydrogen bonds · protein-protein
A–D · 2819 Å² buried · 83 hydrogen bonds · protein-protein

Compared structures

6RT0 · cryo-em structure of alpha-synuclein fibril polymorph 2A · the same entry in another collection · chain A against A, TM-score 1.00

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 6RT0 · PDBe 6RT0 · UniProt P37840

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