[English] 日本語
Yorodumi
- PDB-6jk6: Crystal structure of human chitotriosidase-1 (hCHIT) catalytic do... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jk6
TitleCrystal structure of human chitotriosidase-1 (hCHIT) catalytic domain in complex with compound 2-8-s2
ComponentsChitotriosidase-1
KeywordsHYDROLASE / chitnase / complex / chitotriosidase
Function / homology
Function and homology information


polysaccharide digestion / Digestion of dietary carbohydrate / chitinase activity / endochitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / response to bacterium ...polysaccharide digestion / Digestion of dietary carbohydrate / chitinase activity / endochitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / response to bacterium / specific granule lumen / tertiary granule lumen / lysosome / immune response / Neutrophil degranulation / extracellular space / extracellular region
Similarity search - Function
Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / : / Chitinase insertion domain superfamily / Chitinase II ...Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / : / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-BV0 / Chitotriosidase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.571 Å
AuthorsJiang, X. / Yang, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31425021 China
CitationJournal: J.Med.Chem. / Year: 2020
Title: A Series of Compounds Bearing a Dipyrido-Pyrimidine Scaffold Acting as Novel Human and Insect Pest Chitinase Inhibitors.
Authors: Jiang, X. / Kumar, A. / Motomura, Y. / Liu, T. / Zhou, Y. / Moro, K. / Zhang, K.Y.J. / Yang, Q.
History
DepositionFeb 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: 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 1.2Nov 22, 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
Revision 1.3Nov 20, 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: Chitotriosidase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5603
Polymers42,6691
Non-polymers8912
Water6,395355
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.726, 66.726, 88.363
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein Chitotriosidase-1 / Chitinase-1


Mass: 42668.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHIT1 / Plasmid: pPIC9 / Production host: Komagataella phaffii GS115 (fungus) / Strain (production host): GS115 / References: UniProt: Q13231, chitinase
#2: Chemical ChemComp-BV0 / 6-azanyl-11-methyl-2-oxidanylidene-7-[[(2R)-oxolan-2-yl]methyl]-N-(pyridin-3-ylmethyl)-1,9-diaza-7-azoniatricyclo[8.4.0.0^{3,8}]tetradeca-3(8),4,6,9,11,13-hexaene-5-carboxamide


Mass: 445.494 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H25N6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 25% (w/v) polyethylene glycol (PEG) 3350, 0.2 M potassium sodium tartrate (PST), pH 7.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97778 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97778 Å / Relative weight: 1
ReflectionResolution: 1.571→36.838 Å / Num. obs: 53832 / % possible obs: 99.96 % / Redundancy: 7.4 % / Rsym value: 0.057 / Net I/σ(I): 37.03
Reflection shellResolution: 1.571→1.6 Å / Mean I/σ(I) obs: 16.15 / Num. unique obs: 2678 / Rsym value: 0.133

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WK9

4wk9


Resolution: 1.571→29.84 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.22
RfactorNum. reflection% reflection
Rfree0.1875 2012 3.74 %
Rwork0.1662 --
obs0.167 53781 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.571→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2861 0 66 355 3282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093008
X-RAY DIFFRACTIONf_angle_d1.0034085
X-RAY DIFFRACTIONf_dihedral_angle_d15.6151093
X-RAY DIFFRACTIONf_chiral_restr0.058420
X-RAY DIFFRACTIONf_plane_restr0.006524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5714-1.61070.21471390.19963674X-RAY DIFFRACTION100
1.6107-1.65420.22281470.19313695X-RAY DIFFRACTION100
1.6542-1.70290.221410.18553693X-RAY DIFFRACTION100
1.7029-1.75790.18311420.18163711X-RAY DIFFRACTION100
1.7579-1.82070.23381450.17233671X-RAY DIFFRACTION100
1.8207-1.89360.19451370.17273651X-RAY DIFFRACTION100
1.8936-1.97970.20771430.17453711X-RAY DIFFRACTION100
1.9797-2.08410.21581460.17643721X-RAY DIFFRACTION100
2.0841-2.21470.18841460.16883670X-RAY DIFFRACTION100
2.2147-2.38560.19141400.16623694X-RAY DIFFRACTION100
2.3856-2.62570.17621450.16963714X-RAY DIFFRACTION100
2.6257-3.00540.1881450.16633706X-RAY DIFFRACTION100
3.0054-3.78590.16631430.15013705X-RAY DIFFRACTION100
3.7859-29.840.16561530.15053753X-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