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Crystal structure of the enantiomer of a macrocyclic peptide containing fragments from alpha synuclein 36-55

Analyse Crystal structure of the enantiomer of a macrocyclic peptide containing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5F1W
Type: protein
Length: 96 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Macrocyclic peptide
Ligands: SO4

Structure

x-ray diffraction · 1 distinct chain · 0% helix, 63% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Macrocyclic peptide	protein	16	0% helix, 63% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · chains B, D
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains B, E, A, C

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

Interfaces

6 interfaces between chains.

D–E · 283 Å² buried · 5 hydrogen bonds · protein-protein
A–F · 280 Å² buried · 6 hydrogen bonds · protein-protein
B–E · 272 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 222 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 133 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 60 d-amino, 24 modified (D-amino acid, nonstandard).

Compared structures

5F1W · Crystal structure of the enantiomer of a macrocyclic peptide containing fragments from… · 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 5F1W · PDBe 5F1W

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