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- PDB-7cm0: Crystal structure of a glutaminyl cyclase in complex with NHV-1009 -

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Basic information

Entry
Database: PDB / ID: 7cm0
TitleCrystal structure of a glutaminyl cyclase in complex with NHV-1009
ComponentsGlutaminyl-peptide cyclotransferase
KeywordsTRANSFERASE / glutaminyl cyclases (QCs) / Alzheimer disease
Function / homology
Function and homology information


peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase activity / protein modification process / specific granule lumen / tertiary granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular exosome / extracellular region / zinc ion binding
Similarity search - Function
M28 Zn-Peptidase Glutaminyl Cyclase / Glutaminyl-peptide cyclotransferase-like / Peptidase M28 / Peptidase family M28
Similarity search - Domain/homology
Chem-G5R / Glutaminyl-peptide cyclotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLee, J.W. / Song, J.Y. / Jang, T.H. / Ha, J.H.
CitationJournal: Eur.J.Med.Chem. / Year: 2021
Title: Discovery of highly potent human glutaminyl cyclase (QC) inhibitors as anti-Alzheimer's agents by the combination of pharmacophore-based and structure-based design.
Authors: Van Manh, N. / Hoang, V.H. / Ngo, V.T.H. / Ann, J. / Jang, T.H. / Ha, J.H. / Song, J.Y. / Ha, H.J. / Kim, H. / Kim, Y.H. / Lee, J. / Lee, J.
History
DepositionJul 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutaminyl-peptide cyclotransferase
B: Glutaminyl-peptide cyclotransferase
C: Glutaminyl-peptide cyclotransferase
D: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,85712
Polymers149,5974
Non-polymers2,2608
Water2,810156
1
A: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9643
Polymers37,3991
Non-polymers5652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9643
Polymers37,3991
Non-polymers5652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9643
Polymers37,3991
Non-polymers5652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9643
Polymers37,3991
Non-polymers5652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.896, 116.896, 99.459
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Space group name HallP3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
Components on special symmetry positions
IDModelComponents
11D-509-

HOH

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Components

#1: Protein
Glutaminyl-peptide cyclotransferase / Glutaminyl cyclase / sQC / Glutaminyl-tRNA cyclotransferase / Glutamyl cyclase / EC


Mass: 37399.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: QPCT / Production host: Escherichia coli (E. coli)
References: UniProt: Q16769, glutaminyl-peptide cyclotransferase
#2: Chemical
ChemComp-G5R / 1-(cyclopentylmethyl)-1-[3-methoxy-4-(2-morpholin-4-ylethoxy)phenyl]-3-[3-(5-methylimidazol-1-yl)propyl]urea


Mass: 499.646 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H41N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 291 K / Method: liquid diffusion / Details: 4M Ammonium acetate, pH 7.0, 0.1M Bis-Tris propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.2→35.47 Å / Num. obs: 77174 / % possible obs: 99.46 % / Redundancy: 11.5 % / CC1/2: 0.861 / Net I/σ(I): 14.3
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 35430 / CC1/2: 0.861

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YWY

4ywy


Resolution: 2.2→33.74 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3346 3811 -
Rwork0.2903 --
obs-77174 96.97 %
Displacement parametersBiso mean: 44.65 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10228 0 148 156 10532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008810712
X-RAY DIFFRACTIONf_angle_d1.152914596
X-RAY DIFFRACTIONf_chiral_restr0.07291572
X-RAY DIFFRACTIONf_plane_restr0.00921888
X-RAY DIFFRACTIONf_dihedral_angle_d19.00683916
LS refinement shellResolution: 2.2→2.279 Å
RfactorNum. reflection% reflection
Rfree0.3346 353 -
Rwork0.2903 7022 -
obs--90.9 %

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