4F9V

Structure of C113A/C136A mutant variant of glycosylated glutaminyl cyclase from Drosophila melanogaster

• PDB DOI: https://doi.org/10.2210/pdb4F9V/pdb

• Classification: TRANSFERASE, HYDROLASE
• Organism(s): Drosophila melanogaster
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2012-05-21 Released: 2012-08-29 
• Deposition Author(s): Kolenko, P., Koch, B., Ruiz-Carilo, D., Stubbs, M.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.215 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 73.25 kDa 
• Atom Count: 5,727 
• Modelled Residue Count: 606 
• Deposited Residue Count: 624 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CG32412	A, B	312	Drosophila melanogaster	Mutation(s): 2  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
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G07617FP GlyCosmos:  G07617FP GlyGen:  G07617FP

Entity ID: 3
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	D	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PBD	F [auth A], H [auth B]	1-(3,4-dimethoxyphenyl)-3-[3-(1H-imidazol-1-yl)propyl]thiourea C15 H20 N4 O2 S FZQXMGLQANXZRP-UHFFFAOYSA-N
PEG	I [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	E [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
PBD	PDBBind:  4F9V	Ki: 944 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.215 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.865	α = 90
b = 170.865	β = 90
c = 57.236	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-29 
Deposition Author(s): Kolenko, P., Koch, B., Ruiz-Carilo, D., Stubbs, M.T.

Revision History  

• Version 1.0: 2012-08-29
  Type: Initial release
  
• Version 1.1: 2012-09-26
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary