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- PDB-5qbx: Crystal structure of human Cathepsin-S with bound ligand -

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Basic information

Entry
Database: PDB / ID: 5qbx
TitleCrystal structure of human Cathepsin-S with bound ligand
ComponentsCathepsin S
KeywordsHYDROLASE / D3R / Cathepsin S / Ligand Docking
Function / homology
Function and homology information


cathepsin S / basement membrane disassembly / positive regulation of cation channel activity / antigen processing and presentation of peptide antigen / endolysosome lumen / response to acidic pH / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures ...cathepsin S / basement membrane disassembly / positive regulation of cation channel activity / antigen processing and presentation of peptide antigen / endolysosome lumen / response to acidic pH / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / toll-like receptor signaling pathway / antigen processing and presentation / cysteine-type endopeptidase activator activity involved in apoptotic process / fibronectin binding / collagen catabolic process / extracellular matrix disassembly / phagocytic vesicle / laminin binding / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / positive regulation of apoptotic signaling pathway / protein processing / antigen processing and presentation of exogenous peptide antigen via MHC class II / late endosome / tertiary granule lumen / collagen-containing extracellular matrix / ficolin-1-rich granule lumen / adaptive immune response / lysosome / immune response / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular region
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
Chem-B8V / Cathepsin S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
Model detailsStructures re-refined for D3R docking challenge
AuthorsBembenek, S.D. / Ameriks, M.K. / Mirzadegan, T. / Yang, H. / Shao, C. / Burley, S.K.
CitationJournal: To be published
Title: Crystal structure of human Cathepsin-S with bound ligand
Authors: Bembenek, S.D. / Ameriks, M.K. / Mirzadegan, T. / Yang, H. / Shao, C. / Burley, S.K.
History
DepositionAug 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_type
Revision 2.0Jun 6, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Other / Refinement description / Structure summary
Category: atom_site / atom_sites ...atom_site / atom_sites / computing / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software
Item: _atom_site.Cartn_z / _atom_site.occupancy ..._atom_site.Cartn_z / _atom_site.occupancy / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_poly_seq_scheme.auth_mon_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_obs / _refine.ls_percent_reflns_obs / _refine_hist.cycle_id / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_all / _reflns.percent_possible_obs / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.type
Revision 2.1Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 2.2Nov 17, 2021Group: Database references / Structure summary / Category: database_2 / pdbx_deposit_group
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_deposit_group.group_description
Revision 2.3Oct 9, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cathepsin S
B: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3494
Polymers49,0332
Non-polymers1,3162
Water6,233346
1
A: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1742
Polymers24,5161
Non-polymers6581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1742
Polymers24,5161
Non-polymers6581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.502, 59.579, 56.590
Angle α, β, γ (deg.)100.32, 95.76, 101.20
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 0 - 218 / Label seq-ID: 1 - 219

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Cathepsin S


Mass: 24516.471 Da / Num. of mol.: 2 / Mutation: C139S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSS / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25774, cathepsin S
#2: Chemical ChemComp-B8V / (2S)-1-[4-(2-methoxyphenyl)piperidin-1-yl]-3-{3-[3-{[2-(piperidin-1-yl)ethyl]sulfanyl}-4-(trifluoromethyl)phenyl]-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridin-1-yl}propan-2-ol


Mass: 657.832 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H46F3N5O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 100MM SODIUM ACETATE PH 4.5, 200MM AMMONIUM ACETATE, 25% PEG 8000. PROTEIN CONCENTRATION 7 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→28.61 Å / Num. obs: 21171 / % possible obs: 88.8 %

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0158refinement
PDB_EXTRACT3.23data extraction
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→28.61 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.054 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.337 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1157 5.2 %RANDOM
Rwork0.188 ---
obs0.19 21171 88.8 %-
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: 31.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å2-0.05 Å2-0.03 Å2
2--0.12 Å2-0.34 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3382 0 92 346 3820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023574
X-RAY DIFFRACTIONr_bond_other_d0.0020.023126
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.9294848
X-RAY DIFFRACTIONr_angle_other_deg0.9832.9877283
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6035436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.75224.375160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52615548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1061514
X-RAY DIFFRACTIONr_chiral_restr0.0790.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024008
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02752
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 14894 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 71 -
Rwork0.293 1202 -
obs--68.4 %

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