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- PDB-3hha: Crystal structure of cathepsin L in complex with AZ12878478 -

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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 / zymogen activation / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / cysteine-type endopeptidase activator activity involved in apoptotic process / antigen processing and presentation / protein autoprocessing / Collagen degradation / 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 / lysosome / Attachment and Entry / immune response / symbiont entry into host cell / apical plasma membrane / cysteine-type endopeptidase activity / fusion of virus membrane with host plasma membrane / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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Components

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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

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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

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Details

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

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Experimental details

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Experiment

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

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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

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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

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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 %

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