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- PDB-9ivv: Crystal structure of human secretory glutaminyl cyclase in comple... -

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Basic information

Entry
Database: PDB / ID: 9ivv
TitleCrystal structure of human secretory glutaminyl cyclase in complex with the inhibitor 3-((2-(1H-imidazol-5-yl)ethyl)carbamoyl)-4-amino-1,2,5-oxadiazole 2-oxide (compound 13)
ComponentsGlutaminyl-peptide cyclotransferase
KeywordsTRANSFERASE / glutaminyl cyclase / inhibitor / complex
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
: / DIMETHYLFORMAMIDE / Glutaminyl-peptide cyclotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.961 Å
AuthorsLi, G.-B. / Yu, J.-L. / Zhou, C. / Ning, X.-L. / Mou, J. / Wu, J.-W. / Meng, F.-B.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82073698 China
National Natural Science Foundation of China (NSFC)82073698 China
CitationJournal: Nat Commun / Year: 2025
Title: Knowledge-guided diffusion model for 3D ligand-pharmacophore mapping.
Authors: Yu, J.L. / Zhou, C. / Ning, X.L. / Mou, J. / Meng, F.B. / Wu, J.W. / Chen, Y.T. / Tang, B.D. / Liu, X.G. / Li, G.B.
History
DepositionJul 24, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,45910
Polymers37,5571
Non-polymers9019
Water64936
1
A: Glutaminyl-peptide cyclotransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)230,75260
Polymers225,3446
Non-polymers5,40854
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
Buried area15490 Å2
ΔGint-3 kcal/mol
Surface area71440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)274.600, 274.600, 274.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 37557.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Human / Source: (gene. exp.) Homo sapiens (human) / Gene: QPCT / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q16769, glutaminyl-peptide cyclotransferase

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Non-polymers , 6 types, 45 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1D94 / 4-azanyl-~{N}-[2-(1~{H}-imidazol-4-yl)ethyl]-2-oxidanidyl-1,2,5-oxadiazol-2-ium-3-carboxamide / STK779818


Mass: 238.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10N6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Chemical ChemComp-DMF / DIMETHYLFORMAMIDE


Mass: 73.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 5.84 Å3/Da / Density % sol: 78.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12-16% (v/v) polyethylene glycol 4000, 0.2 M MgCl2 and 0.1 M Tris-HCl at pH 8.5.

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Data collection

DiffractionMean temperature: 195 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.96→34.33 Å / Num. obs: 19047 / % possible obs: 99.9 % / Redundancy: 76.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.56 / Rpim(I) all: 0.064 / Rrim(I) all: 0.564 / Χ2: 0.99 / Net I/σ(I): 12.3 / Num. measured all: 1460010
Reflection shellResolution: 2.96→3.04 Å / % possible obs: 100 % / Redundancy: 80.1 % / Rmerge(I) obs: 4.906 / Num. measured all: 111460 / Num. unique obs: 1392 / CC1/2: 0.628 / Rpim(I) all: 0.549 / Rrim(I) all: 4.937 / Χ2: 0.96 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Aimlessdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PBB

3pbb


Resolution: 2.961→34.325 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2552 1903 10 %
Rwork0.206 --
obs0.2109 19022 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.961→34.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2610 0 55 36 2701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0232740
X-RAY DIFFRACTIONf_angle_d1.3253712
X-RAY DIFFRACTIONf_dihedral_angle_d16.1211608
X-RAY DIFFRACTIONf_chiral_restr0.077391
X-RAY DIFFRACTIONf_plane_restr0.009481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9611-3.03510.36441340.30521204X-RAY DIFFRACTION100
3.0351-3.11710.35741320.2881189X-RAY DIFFRACTION100
3.1171-3.20880.35071310.27751185X-RAY DIFFRACTION100
3.2088-3.31230.30711340.27271197X-RAY DIFFRACTION100
3.3123-3.43050.31871340.25151209X-RAY DIFFRACTION100
3.4305-3.56770.2841330.23981198X-RAY DIFFRACTION100
3.5677-3.72990.27921330.21921197X-RAY DIFFRACTION100
3.7299-3.92630.27141330.21221203X-RAY DIFFRACTION100
3.9263-4.17190.24851350.17481209X-RAY DIFFRACTION100
4.1719-4.49340.19911360.16581226X-RAY DIFFRACTION100
4.4934-4.94440.19911370.15131230X-RAY DIFFRACTION100
4.9444-5.65710.18731380.17041239X-RAY DIFFRACTION100
5.6571-7.11690.2371410.20241273X-RAY DIFFRACTION100
7.1169-34.3250.26561520.20841360X-RAY DIFFRACTION100

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