[English] 日本語
Yorodumi
- PDB-9gc1: CRYSTAL STRUCTURE OF HUMAN CHYMASE IN COMPLEX WITH COMPOUND8 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9gc1
TitleCRYSTAL STRUCTURE OF HUMAN CHYMASE IN COMPLEX WITH COMPOUND8
ComponentsChymase
KeywordsHYDROLASE / SERINE PROTEASE / GLYCOSYLATED / MAST CELLS / SECRETED / HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


chymase / basement membrane disassembly / cytokine precursor processing / peptide metabolic process / Activation of Matrix Metalloproteinases / midbrain development / extracellular matrix disassembly / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / serine-type peptidase activity ...chymase / basement membrane disassembly / cytokine precursor processing / peptide metabolic process / Activation of Matrix Metalloproteinases / midbrain development / extracellular matrix disassembly / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / serine-type peptidase activity / peptide binding / secretory granule / protein maturation / cellular response to glucose stimulus / protein catabolic process / Signaling by SCF-KIT / cytoplasmic ribonucleoprotein granule / positive regulation of angiogenesis / : / regulation of inflammatory response / endopeptidase activity / serine-type endopeptidase activity / extracellular space / extracellular region / cytosol
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.987 Å
AuthorsSchaefer, M. / Fuerstner, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: Discovery and Preclinical Characterization of Fulacimstat (BAY 1142524), a Potent and Selective Chymase Inhibitor As a New Profibrinolytic Approach for Safe Thrombus Resolution.
Authors: Furstner, C. / Ackerstaff, J. / Meier, H. / Straub, A. / Mittendorf, J. / Schamberger, J. / Schafer, M. / Borngen, K. / Jorissen, H. / Zubov, D. / Zimmermann, K. / Tersteegen, A. / Geiss, V. ...Authors: Furstner, C. / Ackerstaff, J. / Meier, H. / Straub, A. / Mittendorf, J. / Schamberger, J. / Schafer, M. / Borngen, K. / Jorissen, H. / Zubov, D. / Zimmermann, K. / Tersteegen, A. / Geiss, V. / Hartmann, E. / Albrecht-Kupper, B. / D'Orleans-Juste, P. / Lapointe, C. / Vincent, L. / Heitmeier, S. / Tinel, H.
History
DepositionAug 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Chymase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2316
Polymers25,0201
Non-polymers1,2115
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-50 kcal/mol
Surface area10730 Å2
Unit cell
Length a, b, c (Å)74.098, 74.098, 49.509
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

-
Components

-
Protein , 1 types, 1 molecules AAA

#1: Protein Chymase / Alpha-chymase / Mast cell protease I


Mass: 25019.871 Da / Num. of mol.: 1 / Mutation: F127K, V208A, R235Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CMA1, CYH, CYM
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: P23946, chymase

-
Sugars , 2 types, 2 molecules

#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.: 1
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
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 3 types, 214 molecules

#4: Chemical ChemComp-A1IJO / 1-(4-methoxyphenyl)-3-[[2-methyl-3-(trifluoromethyl)phenyl]methyl]-2,4-bis(oxidanylidene)pyrimidine-5-carboxylic acid


Mass: 434.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H17F3N2O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.72 Å3/Da / Density % sol: 54.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.01M ZnCl2, 0.1M TRIS at pH 8 and 20% PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.97→29.67 Å / Num. obs: 588899 / % possible obs: 92.22 % / Redundancy: 10.31 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.1598
Reflection shellResolution: 1.97→2.08 Å / Redundancy: 8.67 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.57 / Num. unique obs: 17031 / % possible all: 71.04

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.987→29.663 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.91 / Cross valid method: FREE R-VALUE / ESU R: 0.168 / ESU R Free: 0.151
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2143 907 5.151 %
Rwork0.174 16702 -
all0.176 --
obs-17609 94.216 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.286 Å2
Baniso -1Baniso -2Baniso -3
1--0.012 Å20 Å20 Å2
2---0.012 Å20 Å2
3---0.023 Å2
Refinement stepCycle: LAST / Resolution: 1.987→29.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1662 0 75 211 1948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121780
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.7022410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0545213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.94120.83384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.62415290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7841513
X-RAY DIFFRACTIONr_chiral_restr0.0740.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021317
X-RAY DIFFRACTIONr_nbd_refined0.2160.2823
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21192
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2157
X-RAY DIFFRACTIONr_metal_ion_refined0.0620.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2150.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1910.216
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0470.22
X-RAY DIFFRACTIONr_mcbond_it1.8942.4858
X-RAY DIFFRACTIONr_mcangle_it2.6983.591069
X-RAY DIFFRACTIONr_scbond_it3.2352.991922
X-RAY DIFFRACTIONr_scangle_it5.0914.3141341
X-RAY DIFFRACTIONr_lrange_it7.07435.9222743
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.987-2.0390.234540.2269480.22613600.9150.91973.67650.202
2.039-2.0940.213640.19611910.19713340.9380.92594.0780.174
2.094-2.1550.224590.17311540.17613130.9230.93592.38390.152
2.155-2.2210.233620.18911410.19212580.9170.92795.6280.166
2.221-2.2930.284660.18710690.19312110.8880.92193.72420.165
2.293-2.3730.3490.18110670.18611800.8740.93294.57630.157
2.373-2.4620.182560.17110400.17111490.9470.94895.38730.145
2.462-2.5620.206510.1779890.17810900.9340.94195.41280.153
2.562-2.6750.223540.1819560.18410490.9330.93296.28220.159
2.675-2.8040.229590.1769150.17910080.9140.9496.6270.15
2.804-2.9540.21480.1768770.1789650.930.94995.85490.153
2.954-3.1320.165490.1678380.1679190.9650.95496.5180.152
3.132-3.3450.197370.1617980.1638600.9530.95797.0930.147
3.345-3.6090.188460.1697350.177980.9510.95697.86970.156
3.609-3.9480.16380.1576850.1577370.9640.96398.10040.147
3.948-4.4040.227370.146280.1446770.9460.9798.22750.132
4.404-5.0670.12190.1455730.1446060.9750.96797.68980.14
5.067-6.1610.263180.1825000.1855240.9320.95898.8550.168
6.161-8.5310.229220.2223640.2223910.9280.92798.72120.203
8.531-29.6630.354190.2222340.2322540.8420.91399.60630.227

+
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