6YMB

MicroED structure of human carbonic anhydrase II


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 2.50 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Visualizing drug binding interactions using microcrystal electron diffraction.

Clabbers, M.T.B.Fisher, S.Z.Coincon, M.Zou, X.Xu, H.

(2020) Commun Biol 3: 417-417

  • DOI: 10.1038/s42003-020-01155-1
  • Primary Citation of Related Structures:  
    6YMB, 6YMA

  • PubMed Abstract: 
  • Visualizing ligand binding interactions is important for structure-based drug design and fragment-based screening methods. Rapid and uniform soaking with potentially reduced lattice defects make small macromolecular crystals attractive targets for studying drug binding using microcrystal electron diffraction (MicroED) ...

    Visualizing ligand binding interactions is important for structure-based drug design and fragment-based screening methods. Rapid and uniform soaking with potentially reduced lattice defects make small macromolecular crystals attractive targets for studying drug binding using microcrystal electron diffraction (MicroED). However, so far no drug binding interactions could unambiguously be resolved by electron diffraction alone. Here, we use MicroED to study the binding of a sulfonamide inhibitor to human carbonic anhydrase isoform II (HCA II). We show that MicroED data can efficiently be collected on a conventional transmission electron microscope from thin hydrated microcrystals soaked with the clinical drug acetazolamide (AZM). The data are of high enough quality to unequivocally fit and resolve the bound inhibitor. We anticipate MicroED can play an important role in facilitating in-house fragment screening for drug discovery, complementing existing methods in structural biology such as X-ray and neutron diffraction.


    Organizational Affiliation

    Department of Materials and Environmental Chemistry, Stockholm University, 106 91, Stockholm, Sweden. hongyi.xu@mmk.su.se.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
carbonic anhydrase 2A260Homo 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 2.50 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 
  • Space Group: P 1 21 1
  • Diffraction Data DOI: 10.15785/SBGRID/793 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.51α = 90
b = 41.29β = 104.583
c = 72.79γ = 90
Software Package:
Software NamePurpose
phenix.refinerefinement
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2017-05333
Swedish Research CouncilSweden2019-00815
Knut and Alice Wallenberg FoundationSweden2018.0237

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-12
    Type: Initial release