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Cryo-EM structure of amyloid fibril formed by full-length human SOD1

Analyse Cryo-EM structure of amyloid fibril formed by full-length human SOD1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7VZF
Type: protein
Length: 363 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Superoxide dismutase [cu-zn]
EC: 1.15.1.1
UniProt: P00441
Pockets: 6 · best druggability 0.48

Structure

electron microscopy · 1 distinct chain · 0% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Superoxide dismutase [cu-zn] (EC 1.15.1.1)	protein	121	0% helix, 38% strand	P00441

Pockets

6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	171	0.48	0.76	23	empty
2	62	0.47	0.84	15	empty
3	104	0.45	0.79	22	empty
4	76	0.42	0.80	12	empty
5	164	0.39	0.72	32	empty

Interfaces

3 interfaces between chains.

B–C · 5642 Å² buried · 166 hydrogen bonds · protein-protein
A–B · 5619 Å² buried · 164 hydrogen bonds · protein-protein
A–C · 684 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

7VZF · Cryo-EM structure of amyloid fibril formed by full-length human SOD1 · 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 P00441
Elsewhere: RCSB PDB 7VZF · PDBe 7VZF · UniProt P00441

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