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

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

PDB
5F1T
Type
protein
Length
96 residues
Chains
6
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Macrocyclic peptide
Ligands
CL, SO4

Structure

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

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, C, D, E, FMacrocyclic peptideprotein160% helix, 63% strand—

Ligands and binding sites

  • CL · Chloride ion · ion · 3 copies · chains A, F, D, E
  • SO4 · Sulfate ion · ion · chains B
  • MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B, E
  • MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A, C

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

Interfaces

6 interfaces between chains.

  • D–E · 294 Ų buried · 5 hydrogen bonds · protein-protein
  • A–F · 285 Ų buried · 6 hydrogen bonds · protein-protein
  • B–E · 263 Ų buried · 5 hydrogen bonds · protein-protein
  • A–C · 225 Ų buried · 5 hydrogen bonds · protein-protein
  • B–C · 130 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 modified (nonstandard, methylation).

Compared structures

  • 5F1T · Crystal structure of a macrocyclic peptide containing fragments from alpha-synuclein… · the same entry in another collection · chain A against A, TM-score 1.00

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