7LIB | pdb_00007lib

X-ray crystal structure of a cyclic peptide containing beta-2-microglobulin (63-69) and a gamma-methylornithine turn unit

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 
    0.208 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 2.0 of the entry. See complete history. 

Literature

An Improved Turn Structure for Inducing beta-Hairpin Formation in Peptides.

Li, X., Sabol, A.L., Wierzbicki, M., Salveson, P.J., Nowick, J.S.

(2021) Angew Chem Int Ed Engl 60: 22776-22782

  • DOI: https://doi.org/10.1002/anie.202105559
  • Primary Citation Related Structures: 
    7LIB

  • PubMed Abstract: 

    Although β-hairpins are widespread in proteins, there is no tool to coax any small peptide to adopt a β-hairpin conformation, regardless of sequence. Here, we report that δ-linked γ(R)-methyl-ornithine ( δ MeOrn) provides an improved β-turn template for inducing a β-hairpin conformation in peptides. We developed a synthesis of protected δ MeOrn as a building block suitable for use in Fmoc-based solid-phase peptide synthesis. The synthesis begins with l-leucine and affords gram quantities of the N α -Boc-N δ -Fmoc-γ(R)-methyl-ornithine building block. X-ray crystallography confirms that the δ MeOrn turn unit adopts a folded structure in a macrocyclic β-hairpin peptide. CD and NMR spectroscopy allow comparison of the δ MeOrn turn template to the δ-linked ornithine ( δ Orn) turn template that we previously introduced and to the popular d-Pro-Gly turn template. These studies show that the folding of the δ MeOrn turn template is substantially better than that of δ Orn and is comparable to d-Pro-Gly.

    • Organizational Affiliation: 
    • Department of Chemistry, University of California Irvine, 4126 Natural Sciences I, Irvine, CA, 92697-2025, USA.

Macromolecule Content 

  • Total Structure Weight: 2.09 kDa 
  • Atom Count: 172 
  • Modeled Residue Count: 16 
  • Deposited Residue Count: 16 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cyclic peptide ORD-TYR-LEU-LEU-PHI-TYR-THR-GLU-GMO-LYS-VAL-THR-MVA-THR-VAL-LYS16synthetic constructMutation(s): 0 

Small Molecules

Modified Residues  4 Unique
IDChains TypeFormula2D DiagramParent
MVA
Query on MVA
A
L-PEPTIDE LINKINGC6 H13 N O2VAL
ORN
Query on ORN
A
L-PEPTIDE LINKINGC5 H12 N2 O2ALA
PHI
Query on PHI
A
L-PEPTIDE LINKINGC9 H10 I N O2PHE
Y1V
Query on Y1V
A
L-PEPTIDE LINKINGC6 H14 N2 O2LEU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free:  0.208 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.574α = 90
b = 38.574β = 90
c = 34.925γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM097562

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-11
    Type: Initial release
  • Version 1.1: 2021-10-20
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations