[English] 日本語
Yorodumi
- PDB-3hha: Crystal structure of cathepsin L in complex with AZ12878478 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hha
TitleCrystal structure of cathepsin L in complex with AZ12878478
ComponentsCathepsin L1
KeywordsHYDROLASE / PROTEROS BIOSTRUCTURES GMBH / Cathepsin L / Inhibitors / Disulfide bond / Glycoprotein / Lysosome / Protease / Thiol protease / Zymogen
Function / homology
Function and homology information


enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus ...enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / zymogen activation / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / antigen processing and presentation / cysteine-type endopeptidase activator activity involved in apoptotic process / Collagen degradation / protein autoprocessing / fibronectin binding / collagen catabolic process / serpin family protein binding / cysteine-type peptidase activity / endocytic vesicle lumen / Attachment and Entry / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / multivesicular body / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / positive regulation of apoptotic signaling pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / histone binding / collagen-containing extracellular matrix / adaptive immune response / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / lysosome / immune response / symbiont entry into host cell / apical plasma membrane / fusion of virus membrane with host plasma membrane / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / fusion of virus membrane with host endosome membrane / Golgi apparatus / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-NOW / TRIETHYLENE GLYCOL / Procathepsin L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.27 Å
AuthorsAsaad, N. / Bethel, P.A. / Coulson, M.D. / Dawson, J. / Ford, S.J. / Gerhardt, S. / Grist, M. / Hamlin, G.A. / James, M.J. / Jones, E.V. ...Asaad, N. / Bethel, P.A. / Coulson, M.D. / Dawson, J. / Ford, S.J. / Gerhardt, S. / Grist, M. / Hamlin, G.A. / James, M.J. / Jones, E.V. / Karoutchi, G.I. / Kenny, P.W. / Morley, A.D. / Oldham, K. / Rankine, N. / Ryan, D. / Wells, S.L. / Wood, L. / Augustin, M. / Krapp, S. / Simader, H. / Steinbacher, S.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Dipeptidyl nitrile inhibitors of Cathepsin L.
Authors: Asaad, N. / Bethel, P.A. / Coulson, M.D. / Dawson, J.E. / Ford, S.J. / Gerhardt, S. / Grist, M. / Hamlin, G.A. / James, M.J. / Jones, E.V. / Karoutchi, G.I. / Kenny, P.W. / Morley, A.D. / ...Authors: Asaad, N. / Bethel, P.A. / Coulson, M.D. / Dawson, J.E. / Ford, S.J. / Gerhardt, S. / Grist, M. / Hamlin, G.A. / James, M.J. / Jones, E.V. / Karoutchi, G.I. / Kenny, P.W. / Morley, A.D. / Oldham, K. / Rankine, N. / Ryan, D. / Wells, S.L. / Wood, L. / Augustin, M. / Krapp, S. / Simader, H. / Steinbacher, S.
History
DepositionMay 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2May 30, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Cathepsin L1
B: Cathepsin L1
C: Cathepsin L1
D: Cathepsin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,67612
Polymers96,6474
Non-polymers2,0298
Water17,889993
1
A: Cathepsin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7984
Polymers24,1621
Non-polymers6373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cathepsin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6953
Polymers24,1621
Non-polymers5342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cathepsin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5452
Polymers24,1621
Non-polymers3831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cathepsin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6373
Polymers24,1621
Non-polymers4762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.260, 62.690, 68.240
Angle α, β, γ (deg.)105.60, 93.22, 115.55
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Cathepsin L1 / Major excreted protein / MEP / Cathepsin L1 heavy chain / Cathepsin L1 light chain


Mass: 24161.676 Da / Num. of mol.: 4 / Fragment: Heavy chain and light chain: UNP residues 76-333 / Mutation: T223A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSL1, CTSL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07711, cathepsin L

-
Non-polymers , 6 types, 1001 molecules

#2: Chemical
ChemComp-NOW / Nalpha-[(3-tert-butyl-1-methyl-1H-pyrazol-5-yl)carbonyl]-N-[(2Z)-2-iminoethyl]-3-methyl-L-phenylalaninamide


Mass: 383.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N5O2
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 993 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Sequence detailsTHE MUTATION LISTED IN SEQADV RECORDS HAS BEEN INTRODUCED BY AUTHORS TO ABOLISH A GLYCOSYLATION SITE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.4 / Details: PEG, pH 7.4, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2007 / Details: LN2 cooled fixed-exit
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.27→44.28 Å / Num. all: 182842 / Num. obs: 182842 / % possible obs: 85.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.5 % / Rmerge(I) obs: 0.034
Reflection shellResolution: 1.27→1.33 Å / Redundancy: 0.4 % / Rmerge(I) obs: 0.098 / % possible all: 65.8

-
Processing

Software
NameVersionClassification
XDLdata collection
MOLREPphasing
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.27→44.28 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.253 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15237 9143 5 %RANDOM
Rwork0.11632 ---
all0.11672 ---
obs0.11812 173697 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.158 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0.25 Å2-0.05 Å2
2--0.26 Å2-0.6 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.27→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6695 0 145 993 7833
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0217327
X-RAY DIFFRACTIONr_bond_other_d0.0010.026139
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.9619958
X-RAY DIFFRACTIONr_angle_other_deg0.81314420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.895935
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70125.132341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.187151154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5191525
X-RAY DIFFRACTIONr_chiral_restr0.0890.2972
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028550
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021519
X-RAY DIFFRACTIONr_nbd_refined0.2290.21642
X-RAY DIFFRACTIONr_nbd_other0.190.26399
X-RAY DIFFRACTIONr_nbtor_refined0.1850.23700
X-RAY DIFFRACTIONr_nbtor_other0.0860.23749
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2671
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.241
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.2145
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3690.2127
X-RAY DIFFRACTIONr_mcbond_it3.10225813
X-RAY DIFFRACTIONr_mcbond_other1.79821882
X-RAY DIFFRACTIONr_mcangle_it3.52837193
X-RAY DIFFRACTIONr_scbond_it4.77943470
X-RAY DIFFRACTIONr_scangle_it5.84262765
X-RAY DIFFRACTIONr_rigid_bond_restr2.449316781
X-RAY DIFFRACTIONr_sphericity_free12.2663997
X-RAY DIFFRACTIONr_sphericity_bonded6.143313252
LS refinement shellResolution: 1.27→1.303 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 448 -
Rwork0.159 8499 -
obs--100 %

+
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