6HZX

Protein-aromatic foldamer complex crystal structure

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

Classification: LYASE
Organism(s): Homo sapiens
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.

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

PubMed: 31257622 Search on PubMed
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.

Macromolecule Content

Total Structure Weight: 67.74 kDa
Atom Count: 4,687
Modelled Residue Count: 514
Deposited Residue Count: 514
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens) Explore P00918 Go to UniProtKB: P00918
GTEx: ENSG00000104267
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00918
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6H0 Query on 6H0 Download Ideal Coordinates CCD File SDF format, chain KA [auth B] SDF format, chain N [auth A] SDF format, chain AA [auth B] SDF format, chain D [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain D [auth A]	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		Interactions Focus chain AA [auth B] Focus chain D [auth A] Focus chain KA [auth B] Focus chain N [auth A] Interactions & Density Focus chain AA [auth B] Focus chain D [auth A] Focus chain KA [auth B] Focus chain N [auth A]
QVE Query on QVE Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain G [auth A] SDF format, chain IA [auth B] SDF format, chain L [auth A] SDF format, chain NA [auth B] SDF format, chain Q [auth A] SDF format, chain SA [auth B] SDF format, chain V [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain V [auth A]	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		Interactions Focus chain DA [auth B] Focus chain G [auth A] Focus chain IA [auth B] Focus chain L [auth A] Focus chain NA [auth B] Focus chain Q [auth A] Focus chain SA [auth B] Focus chain V [auth A] Interactions & Density Focus chain DA [auth B] Focus chain G [auth A] Focus chain IA [auth B] Focus chain L [auth A] Focus chain NA [auth B] Focus chain Q [auth A] Focus chain SA [auth B] Focus chain V [auth A]
QUK Query on QUK Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain W [auth A] SDF format, chain BA [auth B] SDF format, chain JA [auth B] SDF format, chain LA [auth B] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain TA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain W [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain TA [auth B]	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		Interactions Focus chain BA [auth B] Focus chain E [auth A] Focus chain JA [auth B] Focus chain LA [auth B] Focus chain M [auth A] Focus chain O [auth A] Focus chain TA [auth B] Focus chain W [auth A] Interactions & Density Focus chain BA [auth B] Focus chain E [auth A] Focus chain JA [auth B] Focus chain LA [auth B] Focus chain M [auth A] Focus chain O [auth A] Focus chain TA [auth B] Focus chain W [auth A]
QDD Query on QDD Download Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain J [auth A] SDF format, chain QA [auth B] SDF format, chain T [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain T [auth A]	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		Interactions Focus chain GA [auth B] Focus chain J [auth A] Focus chain QA [auth B] Focus chain T [auth A] Interactions & Density Focus chain GA [auth B] Focus chain J [auth A] Focus chain QA [auth B] Focus chain T [auth A]
QVS Query on QVS Download Ideal Coordinates CCD File SDF format, chain OA [auth B] SDF format, chain R [auth A] SDF format, chain EA [auth B] SDF format, chain H [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain H [auth A]	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		Interactions Focus chain EA [auth B] Focus chain H [auth A] Focus chain OA [auth B] Focus chain R [auth A] Interactions & Density Focus chain EA [auth B] Focus chain H [auth A] Focus chain OA [auth B] Focus chain R [auth A]
ZY9 Query on ZY9 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain HA [auth B] SDF format, chain K [auth A] SDF format, chain RA [auth B] SDF format, chain U [auth A] SDF format, chain CA [auth B] SDF format, chain FA [auth B] SDF format, chain I [auth A] SDF format, chain MA [auth B] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain S [auth A] MOL2 format, chain F [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain S [auth A]	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		Interactions Focus chain CA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain HA [auth B] Focus chain I [auth A] Focus chain K [auth A] Focus chain MA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain RA [auth B] Focus chain S [auth A] Focus chain U [auth A] Interactions & Density Focus chain CA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain HA [auth B] Focus chain I [auth A] Focus chain K [auth A] Focus chain MA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain RA [auth B] Focus chain S [auth A] Focus chain U [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain UA [auth B] SDF format, chain VA [auth B] SDF format, chain X [auth A] SDF format, chain Y [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A]	UA [auth B], VA [auth B], X [auth A], Y [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain UA [auth B] Focus chain VA [auth B] Focus chain X [auth A] Focus chain Y [auth A] Interactions & Density Focus chain UA [auth B] Focus chain VA [auth B] Focus chain X [auth A] Focus chain Y [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain Z [auth B] MOL2 format, chain C [auth A] MOL2 format, chain Z [auth B]	C [auth A], Z [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain Z [auth B] Interactions & Density Focus chain C [auth A] Focus chain Z [auth B]

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 = 82.64	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

View Full Validation Report

Ligand Structure Quality Assessment

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 (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