5TGY

NMR structure of holo-PS1


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

De novo design of a hyperstable non-natural protein-ligand complex with sub- angstrom accuracy.

Polizzi, N.F.Wu, Y.Lemmin, T.Maxwell, A.M.Zhang, S.Q.Rawson, J.Beratan, D.N.Therien, M.J.DeGrado, W.F.

(2017) Nat Chem 9: 1157-1164

  • DOI: https://doi.org/10.1038/nchem.2846
  • Primary Citation of Related Structures:  
    5TGW, 5TGY

  • PubMed Abstract: 

    Protein catalysis requires the atomic-level orchestration of side chains, substrates and cofactors, and yet the ability to design a small-molecule-binding protein entirely from first principles with a precisely predetermined structure has not been demonstrated. Here we report the design of a novel protein, PS1, that binds a highly electron-deficient non-natural porphyrin at temperatures up to 100 °C. The high-resolution structure of holo-PS1 is in sub-Å agreement with the design. The structure of apo-PS1 retains the remote core packing of the holoprotein, with a flexible binding region that is predisposed to ligand binding with the desired geometry. Our results illustrate the unification of core packing and binding-site definition as a central principle of ligand-binding protein design.


  • Organizational Affiliation

    Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PS1109Escherichia coliMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7BU
Query on 7BU

Download Ideal Coordinates CCD File 
B [auth A][5,10,15,20-tetrakis(trifluoromethyl)porphyrinato(2-)-kappa~4~N~21~,N~22~,N~23~,N~24~]zinc
C24 H8 F12 N4 Zn
HVSFTYLFHSNRAZ-HQJDZOCDSA-N
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE-1413333
National Science Foundation (NSF, United States)United StatesCHE-1413295
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM-071628
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM-048043

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.2: 2017-12-06
    Changes: Database references
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2023-06-14
    Changes: Database references, Other
  • Version 1.5: 2024-05-15
    Changes: Data collection, Database references