4FWU | pdb_00004fwu

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.208 (Depositor), 0.179 (DCC)
R-Value Work:
0.166 (Depositor), 0.172 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309113005575
Primary Citation 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.

Organizational Affiliation

Department of Physical Biochemistry, Institute of Biochemistry and Biotechnology, MLU, Kurt-Mothes-Strasse 3, 06120 Halle, Germany. petr.kolenko@gmail.com

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9VRQ9
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A	Go to GlyGen: Q9VRQ9-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], H [auth A], J [auth A], K [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain K [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain I [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain I [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.208 (Depositor), 0.179 (DCC)
R-Value Work: 0.166 (Depositor), 0.172 (DCC)
R-Value Observed: 0.170 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2012-09-05

Deposition Author(s):

Kolenko, P.

Koch, B.

Stubbs, M.T.

Revision History (Full details and data files)

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
Version 2.2: 2024-11-06
Changes: Structure summary