6S9Z

Expression tag modified N-terminus of human Carbonic Anhydrase II covalently linked to fragment

• PDB DOI: https://doi.org/10.2210/pdb6S9Z/pdb

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


• Deposited: 2019-07-15 Released: 2020-04-15 
• Deposition Author(s): Gloeckner, S., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free: 0.137 
• R-Value Work: 0.119 
• R-Value Observed: 0.120 

Starting Model: experimental

Literature

A Proof-of-Concept Fragment Screening of a Hit-Validated 96-Compounds Library against Human Carbonic Anhydrase II.

Glockner, S., Heine, A., Klebe, G.

(2020) Biomolecules 10

• PubMed: 32235320 
• DOI: https://doi.org/10.3390/biom10040518
• Primary Citation of Related Structures:  
  5M78, 6RM1, 6RMP, 6S9Z, 6SAC, 6SAS, 6SAY, 6SB7, 6SDJ


• PubMed Abstract: 
  

  Fragment screening is a powerful tool to identify and characterize binding pockets in proteins. We herein present the results of a proof-of-concept screening campaign of a versatile 96-entry fragment library from our laboratory against the drug target and model protein human carbonic anhydrase II. The screening revealed a novel chemotype for carbonic anhydrase inhibition, as well as less common non-covalent interaction types and unexpected covalent linkages. Lastly, different runs of the PanDDA tool reveal a practical hint for its application.

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Organizational Affiliation: 

Institute for Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, 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: 31 kDa 
• Atom Count: 2,904 
• Modelled Residue Count: 265 
• Deposited Residue Count: 265 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	265	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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BE7	G [auth A]	(4-CARBOXYPHENYL)(CHLORO)MERCURY C7 H5 Cl Hg O2 YFZOUMNUDGGHIW-UHFFFAOYSA-M
VKL	H [auth A]	3-[3,4-bis(fluoranyl)phenyl]-5-methyl-1$l^{4},4,5$l^{4},7-tetrazabicyclo[4.3.0]nona-1(6),2,4-triene C12 H12 F2 N4 LPONEBABNALWCF-UHFFFAOYSA-O
HG	B [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
PG4	I [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
DMS	F [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free: 0.137 
• R-Value Work: 0.119 
• R-Value Observed: 0.120 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.354	α = 90
b = 41.28	β = 104.651
c = 72.421	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-15 
Deposition Author(s): Gloeckner, S., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2020-04-15
  Type: Initial release
  
• Version 2.0: 2023-05-24
  Changes: Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary
• Version 2.1: 2024-02-07
  Changes: Data collection, Refinement description
• Version 2.2: 2024-10-16
  Changes: Structure summary