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Cryo-EM structure of human aa amyloid fibril

Analyse Cryo-EM structure of human aa amyloid fibril in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MST
Type: protein
Length: 648 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Serum amyloid a-1 protein
UniProt: P0DJI8
Pockets: 10 · best druggability 0.73

Structure

electron microscopy · 1 distinct chain · 0% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, E, D, F, H, I, J, K, L, G	Serum amyloid a-1 protein	protein	54	0% helix, 46% strand	P0DJI8

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	198	0.73	0.90	34	empty
2	204	0.73	0.89	36	empty
3	122	0.64	0.88	27	empty
4	121	0.62	0.87	29	empty
5	59	0.51	0.86	23	empty

Interfaces

45 interfaces between chains.

A–C · 2557 Å² buried · 76 hydrogen bonds · protein-protein
I–K · 2552 Å² buried · 73 hydrogen bonds · protein-protein
J–L · 2544 Å² buried · 72 hydrogen bonds · protein-protein
B–D · 2537 Å² buried · 72 hydrogen bonds · protein-protein
I–G · 2536 Å² buried · 73 hydrogen bonds · protein-protein

Compared structures

6MST · Cryo-EM structure of human AA amyloid fibril · the same entry in another collection · chain G against G, 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 P0DJI8
Elsewhere: RCSB PDB 6MST · PDBe 6MST · UniProt P0DJI8

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