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Amyloid fibril morphology I (in vitro) from murine SAA1.1 protein

Analyse Amyloid fibril morphology I (in vitro) from murine SAA1.1 protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ZCF
Type: protein
Length: 444 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Serum amyloid a-2 protein
UniProt: P05367
Pockets: 3 · best druggability 0.75

Structure

electron microscopy · 1 distinct chain · 0% helix, 70% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, C, B, A, F, E, H, G, J, I, L, K	Serum amyloid a-2 protein	protein	37	0% helix, 70% strand	P05367

Pockets

3 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	1131	0.75	0.78	84	empty
2	74	0.32	0.74	15	empty
3	69	0.31	0.74	18	empty

Interfaces

34 interfaces between chains.

D–B · 1676 Å² buried · 50 hydrogen bonds · protein-protein
C–E · 1675 Å² buried · 50 hydrogen bonds · protein-protein
D–F · 1674 Å² buried · 50 hydrogen bonds · protein-protein
I–K · 1673 Å² buried · 50 hydrogen bonds · protein-protein
C–A · 1672 Å² buried · 50 hydrogen bonds · protein-protein

Compared structures

6ZCF · Amyloid fibril morphology i (in vitro) from murine SAA1.1 protein · the same entry in another collection · chain K against K, 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 P05367
Elsewhere: RCSB PDB 6ZCF · PDBe 6ZCF · UniProt P05367

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