6HZX | pdb_00006hzx

Protein-aromatic foldamer complex crystal structure

• PDB DOI: https://doi.org/10.2210/pdb6HZX/pdb

• Classification: LYASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-10-24 Released: 2019-09-18 
• Deposition Author(s): Post, S., Langlois d'Estaintot, B., Fischer, L., Granier, T., Huc, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 
  0.210 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

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

• PubMed: 31257622 
• DOI: https://doi.org/10.1002/chem.201902942
• Primary Citation 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.

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Organizational Affiliation: 
• CBMN (UMR5248), Univ. Bordeaux-CNRS-INP, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France.
ARNA (U1212), Univ. Bordeaux-INSERM-CNRS, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France.
Department Pharmazie and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377, München, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A1B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A1B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 67.22 kDa 
• Atom Count: 4,687 
• Modeled Residue Count: 558 
• Deposited Residue Count: 558 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A, B	257	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aromatic foldamer	C, D, E, F	11	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	H [auth A], I [auth A], K [auth B], L [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	G [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  6 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A1IJ4	C, D, E, F	L-PEPTIDE LINKING	C12 H18 N2 O3		--
QDD	C, D, E, F	L-PEPTIDE LINKING	C12 H10 N2 O4		--
QUK	C, D, E, F	L-PEPTIDE LINKING	C13 H15 N3 O3		--
QVE	C, D, E, F	L-PEPTIDE LINKING	C12 H10 N2 O5		--
QVS	C, D, E, F	L-PEPTIDE LINKING	C10 H8 N2 O3		--
ZY9	C, D, E, F	L-PEPTIDE LINKING	C7 H8 N2 O2		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free:  0.210 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.64	α = 90
b = 82.64	β = 90
c = 106.39	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-09-18 
Deposition Author(s): Post, S., Langlois d'Estaintot, B., Fischer, L., Granier, T., Huc, I.

Revision History  

• 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
• Version 3.0: 2024-08-14
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 3.1: 2024-11-06
  Changes: Derived calculations, Structure summary