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

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Basic information

Entry
Database: PDB / ID: 9isd
TitleCrystal structure of human secretory glutaminyl cyclase in complex with the inhibitor N-(1H-benzo[d]imidazol-5-yl)-1-phenylmethanesulfonamide (compound 5)
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 / DI(HYDROXYETHYL)ETHER / Glutaminyl-peptide cyclotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.367 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)82122065 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 17, 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
B: Glutaminyl-peptide cyclotransferase
C: Glutaminyl-peptide cyclotransferase
D: Glutaminyl-peptide cyclotransferase
E: Glutaminyl-peptide cyclotransferase
F: Glutaminyl-peptide cyclotransferase
G: Glutaminyl-peptide cyclotransferase
H: Glutaminyl-peptide cyclotransferase
I: Glutaminyl-peptide cyclotransferase
J: Glutaminyl-peptide cyclotransferase
K: Glutaminyl-peptide cyclotransferase
L: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)496,22346
Polymers491,09312
Non-polymers5,13034
Water25,3471407
1
A: Glutaminyl-peptide cyclotransferase
C: Glutaminyl-peptide cyclotransferase
D: Glutaminyl-peptide cyclotransferase
G: Glutaminyl-peptide cyclotransferase
K: Glutaminyl-peptide cyclotransferase
L: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,01222
Polymers245,5466
Non-polymers2,46616
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20200 Å2
ΔGint-315 kcal/mol
Surface area70760 Å2
MethodPISA
2
F: Glutaminyl-peptide cyclotransferase
H: Glutaminyl-peptide cyclotransferase
I: Glutaminyl-peptide cyclotransferase
J: Glutaminyl-peptide cyclotransferase
hetero molecules

B: Glutaminyl-peptide cyclotransferase
hetero molecules

E: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,21124
Polymers245,5466
Non-polymers2,66418
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
crystal symmetry operation1_666x+1,y+1,z+11
Buried area19990 Å2
ΔGint-329 kcal/mol
Surface area70410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.540, 116.476, 122.750
Angle α, β, γ (deg.)96.21, 114.92, 109.69
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

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


Mass: 40924.406 Da / Num. of mol.: 12
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 , 7 types, 1441 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-A1D93 / N-(1H-benzo[d]imidazol-5-yl)-1-phenylmethanesulfonamide


Mass: 287.337 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C14H13N3O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-DMF / DIMETHYLFORMAMIDE


Mass: 73.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1407 / 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: 2.72 Å3/Da / Density % sol: 54.82 %
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 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.184→39.212 Å / Num. obs: 262894 / % possible obs: 97.84 % / Redundancy: 3.33 % / CC1/2: 0.1964 / CC star: 0.5729 / Rmerge(I) obs: 0.3243 / Rpim(I) all: 0.215 / Rrim(I) all: 0.3912 / Net I/σ(I): 4.95
Reflection shellResolution: 2.184→2.24 Å / Rmerge(I) obs: 1.8774 / Mean I/σ(I) obs: 0.49 / Num. unique obs: 19392 / CC1/2: 0.0903 / CC star: 0.4069 / Rpim(I) all: 1.2764 / Rrim(I) all: 2.2845

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
autoPXV2.0data processing
autoPXV2.0data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PBB

3pbb


Resolution: 2.367→39.212 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2621 1585 0.76 %
Rwork0.1891 --
obs0.1897 208064 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.367→39.212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31320 0 309 1407 33036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02432614
X-RAY DIFFRACTIONf_angle_d1.80144312
X-RAY DIFFRACTIONf_dihedral_angle_d16.49619205
X-RAY DIFFRACTIONf_chiral_restr0.0814692
X-RAY DIFFRACTIONf_plane_restr0.0125750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.367-2.44340.35261380.287618562X-RAY DIFFRACTION98
2.4434-2.53070.33331460.281818652X-RAY DIFFRACTION98
2.5307-2.6320.35571500.274218675X-RAY DIFFRACTION98
2.632-2.75180.37471420.266618638X-RAY DIFFRACTION98
2.7518-2.89680.3341440.246518771X-RAY DIFFRACTION98
2.8968-3.07820.31061460.221918784X-RAY DIFFRACTION99
3.0782-3.31580.29471460.203418802X-RAY DIFFRACTION99
3.3158-3.64930.27581410.179718842X-RAY DIFFRACTION99
3.6493-4.17680.25841430.156218860X-RAY DIFFRACTION99
4.1768-5.26030.19261440.137218926X-RAY DIFFRACTION99
5.2603-39.2120.20541450.170718967X-RAY DIFFRACTION100

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