6HZX

Protein-aromatic foldamer complex crystal structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structure Elucidation of Helical Aromatic Foldamer-Protein Complexes with Large Contact Surface Areas.

Reddy, P.S.Langlois d'Estaintot, B.Granier, T.Mackereth, C.D.Fischer, L.Huc, I.

(2019) Chemistry 25: 11042-11047

  • DOI: https://doi.org/10.1002/chem.201902942
  • Primary Citation of Related Structures:  
    6HZX, 6Q9T

  • PubMed Abstract: 

    The development of large synthetic ligands could be useful to target the sizeable surface areas involved in protein-protein interactions. Herein, we present long helical aromatic oligoamide foldamers bearing proteinogenic side chains that cover up to 450 Å 2 of the human carbonic anhydrase II (HCA) surface. The foldamers are composed of aminoquinolinecarboxylic acids bearing proteinogenic side chains and of more flexible aminomethyl-pyridinecarboxylic acids that enhance helix handedness dynamics. Crystal structures of HCA-foldamer complexes were obtained with a 9- and a 14-mer both showing extensive protein-foldamer hydrophobic contacts. In addition, foldamer-foldamer interactions seem to be prevalent in the crystal packing, leading to the peculiar formation of an HCA superhelix wound around a rod of stacked foldamers. Solution studies confirm the positioning of the foldamer at the protein surface as well as a dimerization of the complexes.


  • Organizational Affiliation

    CBMN (UMR5248), Univ. Bordeaux-CNRS-INP, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2
A, B
257Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1
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
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6H0
Query on 6H0

Download Ideal Coordinates CCD File 
AA [auth B],
D [auth A],
KA [auth B],
N [auth A]
~{N}-[[3-(4-formamidobutoxy)phenyl]methyl]-4-sulfamoyl-benzamide
C19 H23 N3 O5 S
ASGCSQAUBAMMLK-UHFFFAOYSA-N
QVE
Query on QVE

Download Ideal Coordinates CCD File 
DA [auth B]
G [auth A]
IA [auth B]
L [auth A]
NA [auth B]
DA [auth B],
G [auth A],
IA [auth B],
L [auth A],
NA [auth B],
Q [auth A],
SA [auth B],
V [auth A]
8-azanyl-4-(2-hydroxy-2-oxoethyloxy)quinoline-2-carboxylic acid
C12 H10 N2 O5
ISBWTKCQKHNORE-UHFFFAOYSA-N
QUK
Query on QUK

Download Ideal Coordinates CCD File 
BA [auth B]
E [auth A]
JA [auth B]
LA [auth B]
M [auth A]
BA [auth B],
E [auth A],
JA [auth B],
LA [auth B],
M [auth A],
O [auth A],
TA [auth B],
W [auth A]
8-azanyl-4-(3-azanylpropoxy)quinoline-2-carboxylic acid
C13 H15 N3 O3
QGMHWPPZJKLYHR-UHFFFAOYSA-N
QDD
Query on QDD

Download Ideal Coordinates CCD File 
GA [auth B],
J [auth A],
QA [auth B],
T [auth A]
2-(8-azanyl-2-methanoyl-quinolin-4-yl)ethanoic acid
C12 H10 N2 O3
DUFBLPKLVQQBPI-UHFFFAOYSA-N
QVS
Query on QVS

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EA [auth B],
H [auth A],
OA [auth B],
R [auth A]
8-azanyl-4-oxidanyl-quinoline-2-carboxylic acid
C10 H8 N2 O3
KZBXAHDVCSOKJO-UHFFFAOYSA-N
ZY9
Query on ZY9

Download Ideal Coordinates CCD File 
CA [auth B]
F [auth A]
FA [auth B]
HA [auth B]
I [auth A]
CA [auth B],
F [auth A],
FA [auth B],
HA [auth B],
I [auth A],
K [auth A],
MA [auth B],
P [auth A],
PA [auth B],
RA [auth B],
S [auth A],
U [auth A]
6-(aminomethyl)pyridine-2-carboxylic acid
C7 H8 N2 O2
KKWKBQBRQWNTPN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
UA [auth B],
VA [auth B],
X [auth A],
Y [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.64α = 90
b = 82.64β = 90
c = 106.39γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description
  • Version 2.1: 2024-01-24
    Changes: Refinement description