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- PDB-7coz: Crystal Structure of double mutant Y115E Y117E human Secretory Gl... -

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Basic information

Entry
Database: PDB / ID: 7coz
TitleCrystal Structure of double mutant Y115E Y117E human Secretory Glutaminyl Cyclase in complex with LSB-41
ComponentsGlutaminyl-peptide cyclotransferase
KeywordsTRANSFERASE / Glutaminyl-peptide cyclotransferase / sQC / Alzheimer's disease / Pyroglutamate
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 / zinc ion binding / extracellular region
Similarity search - Function
M28 Zn-Peptidase Glutaminyl Cyclase / Glutaminyl-peptide cyclotransferase-like / Peptidase M28 / Peptidase family M28
Similarity search - Domain/homology
Chem-Q39 / Glutaminyl-peptide cyclotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDileep, K.V. / Ihara, K. / Sakai, N. / Shirozu, M. / Zhang, K.Y.J.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16F16385 Japan
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Piperidine-4-carboxamide as a new scaffold for designing secretory glutaminyl cyclase inhibitors.
Authors: Dileep, K.V. / Sakai, N. / Ihara, K. / Kato-Murayama, M. / Nakata, A. / Ito, A. / Sivaraman, D.M. / Shin, J.W. / Yoshida, M. / Shirouzu, M. / Zhang, K.Y.J.
History
DepositionAug 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,87233
Polymers111,9933
Non-polymers2,87830
Water13,980776
1
A: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,22810
Polymers37,3311
Non-polymers8979
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-11 kcal/mol
Surface area13640 Å2
MethodPISA
2
B: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,29111
Polymers37,3311
Non-polymers95910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-10 kcal/mol
Surface area13570 Å2
MethodPISA
3
C: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,35312
Polymers37,3311
Non-polymers1,02211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-10 kcal/mol
Surface area13710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.229, 149.366, 95.377
Angle α, β, γ (deg.)90.000, 97.340, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-509-

HOH

21A-720-

HOH

31A-746-

HOH

41A-757-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 37331.121 Da / Num. of mol.: 3 / Mutation: Y115E, Y117E
Source method: isolated from a genetically manipulated source
Details: Cpd-41 / Source: (gene. exp.) Homo sapiens (human) / Gene: QPCT
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q16769, glutaminyl-peptide cyclotransferase

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Non-polymers , 5 types, 806 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-Q39 / 1-[3-(2-methyl-4-thiophen-2-yl-1,3-thiazol-5-yl)propanoyl]piperidine-4-carboxamide


Mass: 363.498 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H21N3O2S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 776 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 54.85 % / Description: Hexagonal plate like crystals
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100 mM MES buffer pH 6.0-6.5, 46-67 mM NaOH, 100 mM ammonium sulfate
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→43.03 Å / Num. obs: 101712 / % possible obs: 100 % / Redundancy: 7.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.147 / Net I/σ(I): 9.6 / Num. measured all: 773340 / Scaling rejects: 42
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.85-1.887.60.7683797750290.8532.799.9
10.13-43.037.10.07745246410.99821.598.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimless0.5.21data scaling
PDB_EXTRACT3.25data extraction
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YWY

4ywy


Resolution: 1.85→43.03 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2362 5289 5.2 %
Rwork0.1955 --
obs0.1975 101696 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.17 Å2 / Biso mean: 20.7969 Å2 / Biso min: 5.53 Å2
Refinement stepCycle: final / Resolution: 1.85→43.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7759 0 174 776 8709
Biso mean--39.02 26.58 -
Num. residues----978
LS refinement shellResolution: 1.85→1.87 Å
RfactorNum. reflection% reflection
Rfree0.3285 157 -
Rwork0.2557 --
obs-3275 100 %

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