[English] 日本語
Yorodumi
- PDB-8r42: Structure of CHI3L1 in complex with inhibititor 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8r42
TitleStructure of CHI3L1 in complex with inhibititor 2
ComponentsChitinase-3-like protein 1
KeywordsHYDROLASE / Chitinase-3-like-1 / complex protein-inhibitor
Function / homology
Function and homology information


response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / cartilage development / chitin catabolic process / extracellular matrix structural constituent / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / extracellular matrix / response to interleukin-1 ...response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / cartilage development / chitin catabolic process / extracellular matrix structural constituent / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / extracellular matrix / response to interleukin-1 / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-8 production / lung development / specific granule lumen / positive regulation of angiogenesis / cellular response to tumor necrosis factor / carbohydrate binding / carbohydrate metabolic process / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / inflammatory response / Neutrophil degranulation / apoptotic process / perinuclear region of cytoplasm / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
Chitinase insertion domain superfamily / : / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
: / Chitinase-3-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsNowak, E. / Napiorkowska-Gromadzka, A. / Nowotny, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2024
Title: Structure-Based Discovery of High-Affinity Small Molecule Ligands and Development of Tool Probes to Study the Role of Chitinase-3-Like Protein 1.
Authors: Czestkowski, W. / Krzeminski, L. / Piotrowicz, M.C. / Mazur, M. / Pluta, E. / Andryianau, G. / Koralewski, R. / Matyszewski, K. / Olejniczak, S. / Kowalski, M. / Lisiecka, K. / Koziel, R. / ...Authors: Czestkowski, W. / Krzeminski, L. / Piotrowicz, M.C. / Mazur, M. / Pluta, E. / Andryianau, G. / Koralewski, R. / Matyszewski, K. / Olejniczak, S. / Kowalski, M. / Lisiecka, K. / Koziel, R. / Piwowar, K. / Papiernik, D. / Nowotny, M. / Napiorkowska-Gromadzka, A. / Nowak, E. / Niedzialek, D. / Wieczorek, G. / Siwinska, A. / Rejczak, T. / Jedrzejczak, K. / Mulewski, K. / Olczak, J. / Zaslona, Z. / Golebiowski, A. / Drzewicka, K. / Bartoszewicz, A.
History
DepositionNov 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chitinase-3-like protein 1
B: Chitinase-3-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,66218
Polymers85,3492
Non-polymers2,31316
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.480, 121.890, 136.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-412-

CL

21A-560-

HOH

-
Components

-
Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Chitinase-3-like protein 1


Mass: 42674.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHI3L1 / Cell (production host): HEK293 / Production host: Mammalia (mammals) / References: UniProt: P36222
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

-
Non-polymers , 5 types, 120 molecules

#3: Chemical ChemComp-XUC / 2-[4-[(2~{R})-2-[(4-chlorophenyl)methyl]pyrrolidin-1-yl]piperidin-1-yl]pyridine


Mass: 355.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H26ClN3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 17% (v/w) PEG 4000, 0.1 M sodium citrate pH 4.6, 0.2 M ammonium sulfate and 0.1 M DTT

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.32→47.9 Å / Num. obs: 39830 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.999 / Net I/σ(I): 17.6
Reflection shellResolution: 2.32→2.46 Å / Num. unique obs: 6310 / CC1/2: 0.525

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→46.9 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2503 1990 5 %
Rwork0.2047 --
obs0.207 39815 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.32→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5582 0 152 106 5840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045885
X-RAY DIFFRACTIONf_angle_d0.7277982
X-RAY DIFFRACTIONf_dihedral_angle_d6.733858
X-RAY DIFFRACTIONf_chiral_restr0.046865
X-RAY DIFFRACTIONf_plane_restr0.0051017
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.380.38711400.34892668X-RAY DIFFRACTION100
2.38-2.440.36251410.32182662X-RAY DIFFRACTION100
2.44-2.510.31741380.30432634X-RAY DIFFRACTION100
2.51-2.60.37181430.30492714X-RAY DIFFRACTION100
2.6-2.690.36841400.30062667X-RAY DIFFRACTION100
2.69-2.80.34331420.28822685X-RAY DIFFRACTION100
2.8-2.920.31911400.26412670X-RAY DIFFRACTION100
2.92-3.080.32651430.25752707X-RAY DIFFRACTION100
3.08-3.270.3041410.262685X-RAY DIFFRACTION100
3.27-3.520.27851420.2242704X-RAY DIFFRACTION100
3.52-3.880.24241430.19172701X-RAY DIFFRACTION100
3.88-4.440.1921440.16882741X-RAY DIFFRACTION100
4.44-5.590.21761440.16042745X-RAY DIFFRACTION100
5.59-46.90.21371490.17532842X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -40.4242 Å / Origin y: -12.5901 Å / Origin z: 46.4186 Å
111213212223313233
T0.4997 Å20.0023 Å20.0965 Å2-0.3934 Å20.0865 Å2--0.4479 Å2
L1.4061 °2-0.5439 °2-0.1103 °2-1.3401 °20.4534 °2--0.574 °2
S0.0601 Å °-0.0079 Å °-0.1684 Å °0.2918 Å °-0.1251 Å °0.2452 Å °0.1896 Å °-0.0654 Å °0.0668 Å °
Refinement TLS groupSelection details: all

+
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