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Crystal structure of the amyloid-fibril forming peptide kdwsfy derived from human beta 2 microglobulin (58-63)

Analyse Crystal structure of the amyloid-fibril forming peptide kdwsfy derived from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4E0K
Type: protein
Length: 24 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Amyloidogenic peptide segment kdwsfy
Ligands: NA

Structure

x-ray diffraction · 1 distinct chain · 0% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Amyloidogenic peptide segment kdwsfy	protein	6	0% helix, 50% strand	—

Ligands and binding sites

NA · Sodium ion · metal · chains B
PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 2 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

5 interfaces between chains.

C–D · 477 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 464 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 105 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 72 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 46 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4E0K · Crystal Structure of the amyloid-fibril forming peptide KDWSFY derived from human Beta 2… · 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
Elsewhere: RCSB PDB 4E0K · PDBe 4E0K

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