[English] 日本語
Yorodumi
- PDB-8xgb: Crystal structure of human secretory glutaminyl cyclase in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xgb
TitleCrystal structure of human secretory glutaminyl cyclase in complex with (S)-1-(1H-benzo[d]imidazol-5-yl)-5-(4-propoxyphenyl)imidazolidin-2-one
ComponentsGlutaminyl-peptide cyclotransferase
KeywordsTRANSFERASE / 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
: / Glutaminyl-peptide cyclotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 Å
AuthorsLi, G.-B. / Wang, X.-Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82122065;82073698 China
CitationJournal: J.Med.Chem. / Year: 2024
Title: X-ray Structure-Guided Discovery of a Potent Benzimidazole Glutaminyl Cyclase Inhibitor That Shows Activity in a Parkinson's Disease Mouse Model.
Authors: Mou, J. / Ning, X.L. / Wang, X.Y. / Hou, S.Y. / Meng, F.B. / Zhou, C. / Wu, J.W. / Li, C. / Jia, T. / Wu, X. / Wu, Y. / Chen, Y. / Li, G.B.
History
DepositionDec 15, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1173
Polymers37,7161
Non-polymers4022
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.421, 156.421, 80.934
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

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


Mass: 37715.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: QPCT / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q16769, glutaminyl-peptide cyclotransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1D49 / (5~{S})-1-(3~{H}-benzimidazol-5-yl)-5-(4-propoxyphenyl)imidazolidin-2-one / PQ912


Mass: 336.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.05 Å3/Da / Density % sol: 75.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 12% -16% PEG 4000, 0.2M MgCl2, 0.1M Tris HCl, pH 8.5

-
Data collection

DiffractionMean temperature: 195 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 30932 / % possible obs: 94.5 % / Redundancy: 10 % / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.054 / Rrim(I) all: 0.175 / Χ2: 0.897 / Net I/σ(I): 5.8 / Num. measured all: 307970
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.3-2.3480.70412010.7670.9320.2510.750.85673.5
2.34-2.388.50.62112550.8340.9540.2160.6590.8576.4
2.38-2.438.80.54913180.8850.9690.1880.5820.87281.1
2.43-2.489.10.51813970.8840.9690.1770.5480.84183.8
2.48-2.5390.57814040.8920.9710.1980.6120.84387.4
2.53-2.599.10.48314990.9260.9810.1650.5120.83192.4
2.59-2.669.10.43515780.9370.9840.1490.460.82796
2.66-2.739.20.416080.9430.9850.1380.4230.84998.7
2.73-2.8110.30.37916510.9670.9920.1240.3990.815100
2.81-2.910.40.30716360.9780.9940.10.3230.857100
2.9-310.30.2816580.9760.9940.0910.2940.866100
3-3.12110.23716470.9780.9950.0750.2480.863100
3.12-3.2610.90.20116380.9820.9950.0640.2110.855100
3.26-3.4410.70.17716060.9850.9960.0570.1860.867100
3.44-3.6510.10.16116480.9860.9960.0530.170.938100
3.65-3.9310.70.14816450.990.9980.0480.1560.965100
3.93-4.3310.50.14916180.9850.9960.0480.1560.989100
4.33-4.95110.14216440.9870.9970.0450.1490.974100
4.95-6.2410.40.1416520.980.9950.0460.1480.877100
6.24-5010.70.15716290.9760.9940.050.1651.18100

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
SCALEPACKdata scaling
PHASER2.6.0phasing
PDB_EXTRACTdata extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.24→31.241 Å / SU ML: 0.85 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 49.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.4179 970 8.32 %
Rwork0.3211 --
obs0.3292 11658 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.24→31.241 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2610 0 26 6 2642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0232719
X-RAY DIFFRACTIONf_angle_d1.8813697
X-RAY DIFFRACTIONf_dihedral_angle_d15.7971598
X-RAY DIFFRACTIONf_chiral_restr0.075392
X-RAY DIFFRACTIONf_plane_restr0.013480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2401-3.41080.43041330.29751467X-RAY DIFFRACTION96
3.4108-3.62420.40771390.3011555X-RAY DIFFRACTION100
3.6242-3.90350.41421410.30721541X-RAY DIFFRACTION100
3.9035-4.29540.42191380.32381529X-RAY DIFFRACTION100
4.2954-4.91490.43031380.31881530X-RAY DIFFRACTION100
4.9149-6.18440.3951410.33691535X-RAY DIFFRACTION100
6.1844-31.2410.42491400.34741531X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more