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- PDB-5qc3: Crystal structure of human Cathepsin-S with bound ligand -

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Basic information

Entry
Database: PDB / ID: 5qc3
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 / cysteine-type endopeptidase activator activity involved in apoptotic process / fibronectin binding / antigen processing and presentation / collagen catabolic process / extracellular matrix disassembly / laminin binding / phagocytic vesicle / positive regulation of apoptotic signaling pathway / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / proteolysis involved in protein catabolic process / lysosomal lumen / Endosomal/Vacuolar 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 / serine-type endopeptidase activity / intracellular membrane-bounded organelle / 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-B9Y / Cathepsin S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.998 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 1.2Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.3Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,2884
Polymers49,0332
Non-polymers1,2552
Water11,367631
1
A: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1442
Polymers24,5161
Non-polymers6281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1442
Polymers24,5161
Non-polymers6281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.311, 36.953, 127.337
Angle α, β, γ (deg.)90.00, 93.38, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1259-

HOH

21B-1227-

HOH

31B-1228-

HOH

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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-B9Y / 1-{3-[3-{[2-(4-fluoropiperidin-1-yl)ethyl]sulfanyl}-4-(trifluoromethyl)phenyl]-1-[(2S)-2-hydroxy-3-(piperidin-1-yl)propyl]-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl}-2-hydroxyethan-1-one


Mass: 627.737 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H41F4N5O3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 631 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.49 %
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: 1.998→32.835 Å / Num. obs: 28733 / % possible obs: 99.08 %

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX(1.12_2829: ???)refinement
PDB_EXTRACT3.23data extraction
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.998→32.835 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2094 1465 5.1 %
Rwork0.1498 --
obs0.1529 28733 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.998→32.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3406 0 86 631 4123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073590
X-RAY DIFFRACTIONf_angle_d0.9454870
X-RAY DIFFRACTIONf_dihedral_angle_d15.1642084
X-RAY DIFFRACTIONf_chiral_restr0.059488
X-RAY DIFFRACTIONf_plane_restr0.006624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9981-2.06950.26421210.18412605X-RAY DIFFRACTION95
2.0695-2.15240.24241400.17062702X-RAY DIFFRACTION99
2.1524-2.25030.24431370.15792693X-RAY DIFFRACTION99
2.2503-2.36890.23171820.15832671X-RAY DIFFRACTION99
2.3689-2.51730.20921530.16112715X-RAY DIFFRACTION99
2.5173-2.71150.2121470.16022751X-RAY DIFFRACTION100
2.7115-2.98430.19231360.152741X-RAY DIFFRACTION100
2.9843-3.41570.21461460.1422760X-RAY DIFFRACTION100
3.4157-4.30190.1691390.12622775X-RAY DIFFRACTION100
4.3019-32.83960.20431640.14472855X-RAY DIFFRACTION100

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