4MTY

Structure at 1A resolution of a helical aromatic foldamer-protein complex.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.123 
  • R-Value Work: 0.105 
  • R-Value Observed: 0.106 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structure of a complex formed by a protein and a helical aromatic oligoamide foldamer at 2.1 a resolution.

Buratto, J.Colombo, C.Stupfel, M.Dawson, S.J.Dolain, C.Langlois d'Estaintot, B.Fischer, L.Granier, T.Laguerre, M.Gallois, B.Huc, I.

(2014) Angew Chem Int Ed Engl 53: 883-887

  • DOI: https://doi.org/10.1002/anie.201309160
  • Primary Citation of Related Structures:  
    4LP6, 4MTY

  • PubMed Abstract: 

    In the search of molecules that could recognize sizeable areas of protein surfaces, a series of ten helical aromatic oligoamide foldamers was synthesized on solid phase. The foldamers comprise three to five monomers carrying various proteinogenic side chains, and exist as racemic mixtures of interconverting right-handed and left-handed helices. Functionalization of the foldamers by a nanomolar ligand of human carbonic anhydrase II (HCA) ensured that they would be held in close proximity to the protein surface. Foldamer-protein interactions were screened by circular dichroism (CD). One foldamer displayed intense CD bands indicating that a preferred helix handedness is induced upon interacting with the protein surface. The crystal structure of the complex between this foldamer and HCA could be resolved at 2.1 Å resolution and revealed a number of unanticipated protein-foldamer, foldamer-foldamer, and protein-protein interactions.


  • Organizational Affiliation

    Université de Bordeaux, CBMN, UMR 5248, Institut Européen de Chimie Biologie, 2 rue Robert Escarpit 33607 Pessac (France); CNRS, CBMN, UMR5248 (France); Institut Polytechnique de Bordeaux, UMR5248 (France).


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2260Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens)
Explore P00918 
Go to UniProtKB:  P00918
PHAROS:  P00918
GTEx:  ENSG00000104267 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00918
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HGB
Query on HGB

Download Ideal Coordinates CCD File 
E [auth A]4-(HYDROXYMERCURY)BENZOIC ACID
C7 H6 Hg O3
WMHRYLDWLOGHSG-UHFFFAOYSA-M
SBW
Query on SBW

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
K [auth A]
N-(3-hydroxybenzyl)-4-sulfamoylbenzamide
C14 H14 N2 O4 S
JHOGRPZBQMWATN-UHFFFAOYSA-N
HG
Query on HG

Download Ideal Coordinates CCD File 
J [auth A]MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.123 
  • R-Value Work: 0.105 
  • R-Value Observed: 0.106 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.444α = 90
b = 41.559β = 104.41
c = 72.064γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DNAdata collection

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2014-01-22
    Changes: Database references
  • Version 1.2: 2017-07-05
    Changes: Refinement description, Structure summary
  • Version 1.3: 2017-07-19
    Changes: Structure summary
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description