7TML | pdb_00007tml

Porous framework formed by assembly of a bipyridyl-conjugated helical peptide

  • Classification: DE NOVO PROTEIN
  • Organism(s): synthetic construct
  • Mutation(s): No 

  • Deposited: 2022-01-19 Released: 2022-04-20 
  • Deposition Author(s): Nguyen, A.I.
  • Funding Organization(s): Department of Energy (DOE, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.93 Å
  • R-Value Free: 
    0.220 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PIHClick on this verticalbar to view details

This is version 2.0 of the entry. See complete history


Literature

Assembly of pi-Stacking Helical Peptides into a Porous and Multivariable Proteomimetic Framework.

Heinz-Kunert, S.L.Pandya, A.Dang, V.T.Tran, P.N.Ghosh, S.McElheny, D.Santarsiero, B.D.Ren, Z.Nguyen, A.I.

(2022) J Am Chem Soc 144: 7001-7009

  • DOI: https://doi.org/10.1021/jacs.2c02146
  • Primary Citation of Related Structures:  
    7TLS, 7TLU, 7TM1, 7TM2, 7TMA, 7TME, 7TMH, 7TMI, 7TMJ, 7TMK, 7TML

  • PubMed Abstract: 

    The evolution of proteins from simpler, self-assembled peptides provides a powerful blueprint for the design of complex synthetic materials. Previously, peptide-metal frameworks using short sequences (≤3 residues) have shown great promise as proteomimetic materials that exhibit sophisticated capabilities. However, their development has been hindered due to few variable residues and restricted choice of side-chains that are compatible with metal ions. Herein, we developed a noncovalent strategy featuring π-stacking bipyridyl residues to assemble much longer peptides into crystalline frameworks that tolerate even previously incompatible acidic and basic functionalities and allow an unprecedented level of pore variations. Single-crystal X-ray structures are provided for all variants to guide and validate rational design. These materials exhibit hallmark proteomimetic behaviors such as guest-selective induced fit and assembly of multimetallic units. Significantly, we demonstrate facile optimization of the framework design to substantially increase affinity toward a complex organic molecule.


  • Organizational Affiliation

    Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
bipyridyl-conjugated helical peptide11synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
AIB
Query on AIB
A
L-PEPTIDE LINKINGC4 H9 N O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.93 Å
  • R-Value Free:  0.220 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 13.76α = 90
b = 13.394β = 97.651
c = 27.732γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
APEXdata reduction
APEXdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PIHClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data

  • Released Date: 2022-04-20 
  • Deposition Author(s): Nguyen, A.I.

Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)DE-AC02-06CH11357

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-20
    Type: Initial release
  • Version 1.1: 2022-04-27
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection
  • Version 2.0: 2024-09-25
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary