4FWU

Crystal structure of glutaminyl cyclase from drosophila melanogaster in space group I4

• PDB DOI: https://doi.org/10.2210/pdb4FWU/pdb

• Classification: HYDROLASE
• Organism(s): Drosophila melanogaster
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2012-07-02 Released: 2012-09-05 
• Deposition Author(s): Kolenko, P., Koch, B., Stubbs, M.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.208 
• R-Value Work: 0.166 
• R-Value Observed: 0.170 

Literature

Structure of glutaminyl cyclase from Drosophila melanogaster in space group I4.

Kolenko, P., Koch, B., Rahfeld, J.U., Schilling, S., Demuth, H.U., Stubbs, M.T.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 358-361

• PubMed: 23545638 
• DOI: https://doi.org/10.1107/S1744309113005575
• Primary Citation of Related Structures:  
  4FWU


• PubMed Abstract: 
  

  The structure of ligand-free glutaminyl cyclase (QC) from Drosophila melanogaster (DmQC) has been determined in a novel crystal form. The protein crystallized in space group I4, with unit-cell parameters a = b = 122.3, c = 72.7 Å. The crystal diffracted to a resolution of 2 Å at the home source. The structure was solved by molecular replacement and was refined to an R factor of 0.169. DmQC exhibits a typical α/β-hydrolase fold. The electron density of three monosaccharides could be localized. The accessibility of the active site will facilitate structural studies of novel inhibitor-binding modes.

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Organizational Affiliation: 

Department of Physical Biochemistry, Institute of Biochemistry and Biotechnology, MLU, Kurt-Mothes-Strasse 3, 06120 Halle, Germany. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.66 kDa 
• Atom Count: 2,860 
• Modelled Residue Count: 299 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CG32412	A	312	Drosophila melanogaster	Mutation(s): 0  Gene Names: QC, CG10487, CG32412, Dmel_CG32412 EC: 2.3.2.5 (PDB Primary Data), 3.4 (PDB Primary Data)
UniProt
Find proteins for Q9VRQ9 (Drosophila melanogaster) Explore Q9VRQ9  Go to UniProtKB:  Q9VRQ9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth A], G [auth A], H [auth A], J [auth A], K [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.208 
• R-Value Work: 0.166 
• R-Value Observed: 0.170 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.344	α = 90
b = 122.344	β = 90
c = 72.736	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-05 
Deposition Author(s): Kolenko, P., Koch, B., Stubbs, M.T.

Revision History  

• Version 1.0: 2012-09-05
  Type: Initial release
  
• Version 1.1: 2013-04-10
  Changes: Database references
• Version 1.2: 2013-04-17
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary