[English] 日本語
Yorodumi
- PDB-9kwl: hCES1A contently binding with compound F-3 at the catalytic pocket. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9kwl
TitlehCES1A contently binding with compound F-3 at the catalytic pocket.
ComponentsLiver carboxylesterase 1
KeywordsHYDROLASE / hCES1A / Covalent / Inhibitors / SBDD
Function / homology
Function and homology information


cholesterol ester hydrolysis involved in cholesterol transport / methylumbelliferyl-acetate deacetylase / methylumbelliferyl-acetate deacetylase activity / regulation of bile acid secretion / sterol esterase / sterol ester esterase activity / medium-chain fatty acid metabolic process / carboxylesterase / Physiological factors / carboxylesterase activity ...cholesterol ester hydrolysis involved in cholesterol transport / methylumbelliferyl-acetate deacetylase / methylumbelliferyl-acetate deacetylase activity / regulation of bile acid secretion / sterol esterase / sterol ester esterase activity / medium-chain fatty acid metabolic process / carboxylesterase / Physiological factors / carboxylesterase activity / regulation of bile acid biosynthetic process / positive regulation of cholesterol metabolic process / cellular response to cholesterol / reverse cholesterol transport / Phase I - Functionalization of compounds / carboxylic ester hydrolase activity / cholesterol biosynthetic process / negative regulation of cholesterol storage / Aspirin ADME / cellular response to low-density lipoprotein particle stimulus / positive regulation of cholesterol efflux / Metabolism of Angiotensinogen to Angiotensins / lipid catabolic process / lipid droplet / epithelial cell differentiation / cholesterol metabolic process / cholesterol homeostasis / response to toxic substance / endoplasmic reticulum lumen / endoplasmic reticulum / cytosol / cytoplasm
Similarity search - Function
: / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
: / Liver carboxylesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsGai, C. / Zhao, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82204347 China
CitationJournal: Front Chem / Year: 2024
Title: The study of halogen effect on the reactivity of the serine-targeting covalent warheads.
Authors: Gai, C. / Zhang, Y. / Zhang, S. / Hu, X. / Song, Y.Q. / Zhuang, X. / Chai, X. / Zou, Y. / Ge, G.B. / Zhao, Q.
History
DepositionDec 6, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Liver carboxylesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0703
Polymers58,8001
Non-polymers2692
Water10,034557
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-6 kcal/mol
Surface area20320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.469, 110.469, 278.259
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1171-

HOH

21A-1207-

HOH

31A-1252-

HOH

41A-1254-

HOH

51A-1256-

HOH

-
Components

#1: Protein Liver carboxylesterase 1 / Acyl-coenzyme A:cholesterol acyltransferase / ACAT / Brain carboxylesterase hBr1 / Carboxylesterase ...Acyl-coenzyme A:cholesterol acyltransferase / ACAT / Brain carboxylesterase hBr1 / Carboxylesterase 1 / CE-1 / hCE-1 / Cholesteryl ester hydrolase / CEH / Cocaine carboxylesterase / Egasyn / HMSE / Methylumbelliferyl-acetate deacetylase 1 / Monocyte/macrophage serine esterase / Retinyl ester hydrolase / REH / Serine esterase 1 / Triacylglycerol hydrolase / TGH


Mass: 58800.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CES1, CES2, SES1 / Production host: Homo sapiens (human)
References: UniProt: P23141, carboxylesterase, sterol esterase, methylumbelliferyl-acetate deacetylase
#2: Chemical ChemComp-A1EIY / (1R)-1-(3,4-dichlorophenyl)-2,2,2-tris(fluoranyl)ethanol / (R)-1-(3,4-dichlorophenyl)-2,2,2-trifluoroethanol


Mass: 245.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H5Cl2F3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 14.4% PEG8000(w/v), 0.1M MES 6.4, 0.3M CaAc

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.83→78.83 Å / Num. obs: 111183 / % possible obs: 100 % / Redundancy: 12.5 % / Rrim(I) all: 0.205 / Net I/σ(I): 14.6
Reflection shellResolution: 1.83→1.9 Å / Num. unique obs: 57812 / Rrim(I) all: 0.205

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→56.26 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1857 3870 3.48 %
Rwork0.1717 --
obs0.1722 111183 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.83→56.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4139 0 15 557 4711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d5.723563
X-RAY DIFFRACTIONf_chiral_restr0.058641
X-RAY DIFFRACTIONf_plane_restr0.007743
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.850.28011230.27953640X-RAY DIFFRACTION94
1.85-1.880.29341400.27823763X-RAY DIFFRACTION97
1.88-1.90.29521260.26773762X-RAY DIFFRACTION99
1.9-1.930.26511450.25753812X-RAY DIFFRACTION99
1.95-1.980.23291480.23023868X-RAY DIFFRACTION100
1.98-2.010.23261440.21483854X-RAY DIFFRACTION100
2.01-2.050.26191550.21123874X-RAY DIFFRACTION100
2.05-2.080.20661230.19383820X-RAY DIFFRACTION100
2.08-2.120.1971460.19393876X-RAY DIFFRACTION100
2.16-2.210.20951380.17373867X-RAY DIFFRACTION100
2.21-2.250.20871390.18563881X-RAY DIFFRACTION100
2.25-2.310.21591200.18193827X-RAY DIFFRACTION100
2.31-2.360.2241390.18123829X-RAY DIFFRACTION100
2.36-2.430.20661340.18143851X-RAY DIFFRACTION100
2.43-2.50.19141440.17353855X-RAY DIFFRACTION100
2.5-2.580.19371340.18073829X-RAY DIFFRACTION100
2.58-2.670.22061340.17173892X-RAY DIFFRACTION100
2.67-2.780.21731420.16793803X-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