6QEB | pdb_00006qeb

Assessment of a large enzyme-drug complex by proton-detected solid-state NMR without deuteration

• PDB DOI: https://doi.org/10.2210/pdb6QEB/pdb
• BMRB: 34347

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2019-01-07 Released: 2019-02-06 
• Deposition Author(s): Vasa, S.K.

---

Experimental Data Snapshot

• Method: SOLID-STATE NMR
• Conformers Calculated: 20 
• Conformers Submitted: 20 
• Selection Criteria: lowest energy 

Literature

Assessment of a Large Enzyme-Drug Complex by Proton-Detected Solid-State NMR Spectroscopy without Deuteration.

Vasa, S.K., Singh, H., Grohe, K., Linser, R.

(2019) Angew Chem Int Ed Engl 58: 5758-5762

• PubMed: 30688395 
• DOI: https://doi.org/10.1002/anie.201811714
• Primary Citation Related Structures: 
  6QEB


• PubMed Abstract: 
  

  Solid-state NMR spectroscopy has recently enabled structural biology with small amounts of non-deuterated proteins, largely alleviating the classical sample production demands. Still, despite the benefits for sample preparation, successful and comprehensive characterization of complex spin systems in the few cases of higher-molecular-weight proteins has thus far relied on traditional ¹³ C-detected methodology or sample deuteration. Herein we show for a 29 kDa carbonic anhydrase:acetazolamide complex that different aspects of solid-state NMR assessment of a complex spin system can be successfully accessed using a non-deuterated, 500 μg sample in combination with adequate spectroscopic tools. The shown access to protein structure, protein dynamics, as well as biochemical parameters in amino acid sidechains, such as histidine protonation states, will be transferable to proteins that are not expressible in E. coli.

---

Organizational Affiliation: 
• Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany.
Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227, Dortmund, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.58 kDa 
• Atom Count: 2,087 
• Modeled Residue Count: 260 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AZM	C [auth A]	5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE C4 H6 N4 O3 S2 BZKPWHYZMXOIDC-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AZM	BindingDB:  6QEB	Ki: min: 0.01, max: 104 (nM) from 30 assay(s)
		Kd: min: 2.6, max: 46 (nM) from 11 assay(s)
		IC50: min: 0.49, max: 4500 (nM) from 66 assay(s)

Experimental Data & Validation

Experimental Data

• Method: SOLID-STATE NMR
• Conformers Calculated: 20 
• Conformers Submitted: 20 
• Selection Criteria: lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Vasa, S.K.

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 1.1: 2019-03-13
  Changes: Data collection, Database references
• Version 1.2: 2019-04-17
  Changes: Data collection, Database references
• Version 1.3: 2019-08-21
  Changes: Data collection
• Version 1.4: 2023-06-14
  Changes: Database references, Other
• Version 1.5: 2024-06-19
  Changes: Data collection, Database references