[English] 日本語
Yorodumi
- PDB-9kmb: Crystal structure of human glutaminyl cyclase in complex with N-(... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9kmb
TitleCrystal structure of human glutaminyl cyclase in complex with N-(2-(1H-imidazol-5-yl)ethyl)-4-methoxybenzenesulfonamide
ComponentsGlutaminyl-peptide cyclotransferase
KeywordsTRANSFERASE / glutaminyl cyclase / sQC / human secretory glutaminyl cyclase
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: 2.28 Å
AuthorsLi, G.-B. / Wu, J.-W. / Ning, X.-L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Chem.Inf.Model. / Year: 2025
Title: Deciphering Glutaminyl Cyclase Catalytic Pathways Enables Recognition of Anchor Pharmacophores for Inhibitor Discovery.
Authors: Wu, J.W. / Ning, X.L. / Tang, B.D. / Chen, Y.T. / Yang, Z.B. / Meng, F.B. / Zhou, C. / Yu, J.L. / Li, R. / Li, Z. / Li, G.B.
History
DepositionNov 15, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)113,7129
Polymers112,6723
Non-polymers1,0406
Water63135
1
A: Glutaminyl-peptide cyclotransferase
B: Glutaminyl-peptide cyclotransferase
C: Glutaminyl-peptide cyclotransferase
hetero molecules

A: Glutaminyl-peptide cyclotransferase
B: Glutaminyl-peptide cyclotransferase
C: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,42518
Polymers225,3446
Non-polymers2,08012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area12760 Å2
ΔGint-68 kcal/mol
Surface area73670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.575, 147.170, 160.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

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


Mass: 37557.398 Da / Num. of mol.: 3
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.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1EFY / ~{N}-[2-(1~{H}-imidazol-5-yl)ethyl]-4-methoxy-benzenesulfonamide


Mass: 281.331 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H15N3O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 32% to 35% PEG 8000, 0.1 M lithium sulphate, 0.05M sodium acetate(pH 4.5)

-
Data collection

DiffractionMean temperature: 195 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→44.5709 Å / Num. obs: 57541 / % possible obs: 99.75 % / Redundancy: 17 % / Rpim(I) all: 0.064 / Rrim(I) all: 0.2206 / Net I/σ(I): 15.56
Reflection shellResolution: 2.28→2.337 Å / Num. unique obs: 57529 / Rpim(I) all: 0.8011

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
autoPXdata processing
autoPXdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→44.562 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2662 1999 3.47 %
Rwork0.2163 --
obs0.2181 57529 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.28→44.562 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7830 0 60 35 7925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0188134
X-RAY DIFFRACTIONf_angle_d1.33911055
X-RAY DIFFRACTIONf_dihedral_angle_d19.9952961
X-RAY DIFFRACTIONf_chiral_restr0.0721173
X-RAY DIFFRACTIONf_plane_restr0.011437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.3370.38941380.38263848X-RAY DIFFRACTION97
2.337-2.40020.39141410.3423917X-RAY DIFFRACTION100
2.4002-2.47080.3671420.32943947X-RAY DIFFRACTION100
2.4708-2.55060.3821400.31853911X-RAY DIFFRACTION100
2.5506-2.64170.34091420.30433930X-RAY DIFFRACTION100
2.6417-2.74750.3751430.28593973X-RAY DIFFRACTION100
2.7475-2.87250.33181420.27583931X-RAY DIFFRACTION100
2.8725-3.02390.29441430.25893975X-RAY DIFFRACTION100
3.0239-3.21330.30371420.25543940X-RAY DIFFRACTION100
3.2133-3.46130.30321430.22443964X-RAY DIFFRACTION100
3.4613-3.80950.27261430.20943992X-RAY DIFFRACTION100
3.8095-4.36030.23821440.18383992X-RAY DIFFRACTION100
4.3603-5.49190.17291460.15044039X-RAY DIFFRACTION100
5.4919-44.5620.22091500.16664171X-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