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

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Basic information

Entry
Database: PDB / ID: 5qbv
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 / regulation of antigen processing and presentation / 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 ...cathepsin S / regulation of antigen processing and presentation / 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 / collagen catabolic process / fibronectin binding / extracellular matrix disassembly / collagen binding / phagocytic vesicle / laminin binding / Degradation of the extracellular matrix / cysteine-type peptidase activity / MHC class II antigen presentation / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / protein processing / late endosome / tertiary granule lumen / : / adaptive immune response / ficolin-1-rich granule lumen / lysosome / immune response / serine-type endopeptidase activity / cysteine-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-N2D / Cathepsin S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.796 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: Bioorg.Med.Chem.Lett. / Year: 2010
Title: Diazinones as P2 replacements for pyrazole-based cathepsin S inhibitors
Authors: Ameriks, M.K. / Bembenek, S.D. / Burdett, M.T. / Choong, I.C. / Edwards, J.P. / Gebauer, D. / Gu, Y. / Karlsson, L. / Purkey, H.E. / Staker, B.L. / Sun, S. / Thurmond, R.L. / Zhu, J.
History
DepositionAug 4, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionDec 20, 2017ID: 3MPF
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: Structure summary / Category: audit_author / Item: _audit_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
Revision 1.4Oct 16, 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)50,3244
Polymers49,0332
Non-polymers1,2912
Water11,223623
1
A: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1622
Polymers24,5161
Non-polymers6461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1622
Polymers24,5161
Non-polymers6461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)172.391, 34.311, 104.021
Angle α, β, γ (deg.)90.000, 125.270, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 0 through 218)
21(chain B and (resid 0 through 81 or (resid 82...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILELEULEU(chain A and resid 0 through 218)AA0 - 2181 - 219
21ILEILEASNASN(chain B and (resid 0 through 81 or (resid 82...BB0 - 811 - 82
22LYSLYSLYSLYS(chain B and (resid 0 through 81 or (resid 82...BB8283
23ILEILELEULEU(chain B and (resid 0 through 81 or (resid 82...BB0 - 2181 - 219
24ILEILELEULEU(chain B and (resid 0 through 81 or (resid 82...BB0 - 2181 - 219
25ILEILELEULEU(chain B and (resid 0 through 81 or (resid 82...BB0 - 2181 - 219
26ILEILELEULEU(chain B and (resid 0 through 81 or (resid 82...BB0 - 2181 - 219
27ILEILELEULEU(chain B and (resid 0 through 81 or (resid 82...BB0 - 2181 - 219
28ILEILELEULEU(chain B and (resid 0 through 81 or (resid 82...BB0 - 2181 - 219

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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-N2D / N-[2-chloro-5-(1-{3-[4-(6-chloro-3-methyl-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl)piperidin-1-yl]propyl}-6-oxo-1,6-dihydropyridazin-3-yl)benzyl]benzamide


Mass: 645.578 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34Cl2N6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 623 / 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: 2.59 Å3/Da / Density % sol: 52.51 %
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: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorDetector: CCD / Date: Sep 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 46805 / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 8.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.175 / % possible all: 95.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.12_2829refinement
PDB_EXTRACT3.23data extraction
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.796→43.281 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 15.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1723 2369 5.06 %
Rwork0.147 44429 -
obs0.1482 46798 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.59 Å2 / Biso mean: 16.7347 Å2 / Biso min: 5.88 Å2
Refinement stepCycle: final / Resolution: 1.796→43.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3385 0 90 623 4098
Biso mean--19.33 28.44 -
Num. residues----439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083575
X-RAY DIFFRACTIONf_angle_d0.8364851
X-RAY DIFFRACTIONf_chiral_restr0.063485
X-RAY DIFFRACTIONf_plane_restr0.005623
X-RAY DIFFRACTIONf_dihedral_angle_d17.5722071
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2050X-RAY DIFFRACTION7.812TORSIONAL
12B2050X-RAY DIFFRACTION7.812TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7963-1.8330.2391270.20692342246991
1.833-1.87280.21991440.1752541268598
1.8728-1.91640.1711320.149426252757100
1.9164-1.96430.19341430.14925752718100
1.9643-2.01740.19931490.146226272776100
2.0174-2.07680.18821380.143925782716100
2.0768-2.14380.18891260.151926642790100
2.1438-2.22040.18231460.145825432689100
2.2204-2.30930.17151440.147126532797100
2.3093-2.41440.17961470.153225932740100
2.4144-2.54170.16871350.15226322767100
2.5417-2.70090.1631400.151126392779100
2.7009-2.90940.16811520.148226202772100
2.9094-3.20210.16371540.14626352789100
3.2021-3.66530.14821360.134526662802100
3.6653-4.6170.14191280.127326962824100
4.617-43.29350.18711280.154128002928100

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