5L3O

Crystal Structure of Human Carbonic Anhydrase II in Complex with a Quinoline Oligoamide Foldamer

PDB DOI: https://doi.org/10.2210/pdb5L3O/pdb

Classification: Lyase/Inhibitor
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-05-24 Released: 2017-03-01
Deposition Author(s): Jewginski, M., Langlois d'Estaintot, B., Granier, T., Huc, Y.
Funding Organization(s): Polish Ministry of Science and Education

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.236
R-Value Work: 0.207
R-Value Observed: 0.208

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 4.0 of the entry. See complete history.

Literature

Self-Assembled Protein-Aromatic Foldamer Complexes with 2:3 and 2:2:1 Stoichiometries.

Jewginski, M., Granier, T., Langlois d'Estaintot, B., Fischer, L., Mackereth, C.D., Huc, I.

(2017) J Am Chem Soc 139: 2928-2931

PubMed: 28170240 Search on PubMed
DOI: https://doi.org/10.1021/jacs.7b00184
Primary Citation of Related Structures:
5L3O, 5L6K, 5LVS

PubMed Abstract:
The promotion of protein dimerization using the aggregation properties of a protein ligand was explored and shown to produce complexes with unusual stoichiometries. Helical foldamer 2 was synthesized and bound to human carbonic anhydrase (HCA) using a nanomolar active site ligand. Crystal structures show that the hydrophobicity of 2 and interactions of its side chains lead to the formation of an HCA ₂-2 ₃ complex in which three helices of 2 are stacked, two of them being linked to an HCA molecule. The middle foldamer in the stack can be replaced by alternate sequences 3 or 5. Solution studies by CD and NMR confirm left-handedness of the helical foldamers as well as HCA dimerization.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 64.7 kDa
Atom Count: 4,761
Modelled Residue Count: 540
Deposited Residue Count: 544
Unique protein chains: 2

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	260	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00918
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aromatic foldamer	C, D, E, F	6	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain L [auth B]	H [auth A] I [auth A] J [auth A] L [auth B] M [auth B] H [auth A], I [auth A], J [auth A], L [auth B], M [auth B], N [auth B], O [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.236
R-Value Work: 0.207
R-Value Observed: 0.208
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.88	α = 90
b = 54.48	β = 112.79
c = 84.92	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2017-03-01

Deposition Author(s):

Jewginski, M.

Langlois d'Estaintot, B.

Granier, T.

Huc, Y.

Funding Organization	Location	Grant Number
Polish Ministry of Science and Education	Poland	Mobility Plus Program

Revision History (Full details and data files)

Version 1.0: 2017-03-01
Type: Initial release
Version 1.1: 2017-03-15
Changes: Database references
Version 2.0: 2018-12-19
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2019-08-21
Changes: Data collection, Derived calculations
Version 3.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description
Version 3.1: 2024-01-10
Changes: Refinement description
Version 4.0: 2024-09-04
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Source and taxonomy, Structure summary