MolNFT v1 · #163120 · protein

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

6RTB: “Cryo-EM structure of alpha-synuclein fibril polymorph 2B”. Electron microscopy, 5 pockets (best druggability 0.69). MolNFT v1 #163120 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6RTB
Type: protein
Length: 699 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-synuclein
UniProt: P37840
Pockets: 5 · best druggability 0.69

Structure

electron microscopy · 2 distinct chains · 0% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, C, I, J, E, G, B, F, A	Alpha-synuclein	protein	70	0% helix, 44% strand	P37840
D	Alpha-synuclein	protein	69	0% helix, 38% strand	P37840

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	242	0.69	0.85	43	empty
2	63	0.34	0.77	14	empty
3	76	0.30	0.73	14	empty
4	55	0.28	0.74	14	empty
5	53	0.26	0.74	18	empty

Interfaces

19 interfaces between chains.

D–E · 2720 Å² buried · 62 hydrogen bonds · protein-protein
I–J · 2701 Å² buried · 60 hydrogen bonds · protein-protein
C–B · 2701 Å² buried · 61 hydrogen bonds · protein-protein
G–F · 2697 Å² buried · 69 hydrogen bonds · protein-protein
H–G · 2679 Å² buried · 70 hydrogen bonds · protein-protein

Compared structures

6RTB · cryo-em structure of alpha-synuclein fibril polymorph 2B · the same entry in another collection · chain H against H, 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 6RTB · PDBe 6RTB · UniProt P37840

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