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- PDB-2g7y: Human Cathepsin S with inhibitor CRA-16981 -

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Open data


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Basic information

Entry
Database: PDB / ID: 2g7y
TitleHuman Cathepsin S with inhibitor CRA-16981
ComponentsCathepsin S
KeywordsHYDROLASE / papain / cysteine protease / 16981
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 / laminin binding / collagen binding / MHC class II antigen presentation / phagocytic vesicle / 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 / adaptive immune response / ficolin-1-rich granule lumen / 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-MO9 / Cathepsin S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSomoza, J.R.
CitationJournal: To be Published
Title: Human Cathepsin S with inhibitor CRA-16981
Authors: Somoza, J.R.
History
DepositionMar 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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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)50,9354
Polymers50,0122
Non-polymers9232
Water3,261181
1
A: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4672
Polymers25,0061
Non-polymers4611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4672
Polymers25,0061
Non-polymers4611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.457, 85.457, 150.859
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
DetailsThe biological unit is probably the monomer. The asymmetric unit contains two monomers.

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Components

#1: Protein Cathepsin S


Mass: 25006.027 Da / Num. of mol.: 2
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-MO9 / (1R)-2-[(CYANOMETHYL)AMINO]-1-({[2-(DIFLUOROMETHOXY)BENZYL]SULFONYL}METHYL)-2-OXOETHYL MORPHOLINE-4-CARBOXYLATE


Mass: 461.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H21F2N3O7S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.75 Å3/Da / Density % sol: 55.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5
Details: 22.5%-30% PEG 8K, 0.1 M sodium citrate (pH 5.0), 0.2 M ammonium sulfate, VAPOR DIFFUSION, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 38454 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 9.2 % / Rmerge(I) obs: 0.114 / Χ2: 1.063 / Net I/σ(I): 6.8
Reflection shellResolution: 2→2.03 Å / % possible obs: 99.9 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.641 / Num. unique obs: 1926 / Χ2: 0.792 / % possible all: 99.9

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Phasing

Phasing MRRfactor: 0.365 / Cor.coef. Fo:Fc: 0.673
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / FOM work R set: 0.875 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 3616 9.4 %RANDOM
Rwork0.197 ---
obs0.2 36189 93.8 %-
Solvent computationBsol: 42.944 Å2
Displacement parametersBiso mean: 18.912 Å2
Baniso -1Baniso -2Baniso -3
1-1.886 Å20 Å20 Å2
2--1.886 Å20 Å2
3----3.772 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3350 0 62 181 3593
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_bond_d0.006
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2-2.010.23680.216548616
2.01-2.030.243580.229611669
2.03-2.040.228830.212599682
2.04-2.060.287710.224562633
2.06-2.070.308640.24562626
2.07-2.090.227710.196681752
2.09-2.10.193680.21539607
2.1-2.120.245750.192626701
2.12-2.140.268600.196636696
2.14-2.150.255760.183597673
2.15-2.170.189750.182607682
2.17-2.190.264740.186640714
2.19-2.210.212690.191592661
2.21-2.230.26620.182640702
2.23-2.250.263610.198618679
2.25-2.270.21680.212627695
2.27-2.30.242620.193592654
2.3-2.320.256630.176654717
2.32-2.350.254780.204626704
2.35-2.370.285790.194644723
2.37-2.40.241690.198639708
2.4-2.430.243820.2631713
2.43-2.460.218640.195655719
2.46-2.490.265750.187627702
2.49-2.520.234780.192680758
2.52-2.550.315610.221637698
2.55-2.590.208800.194681761
2.59-2.630.258760.194625701
2.63-2.670.252870.216652739
2.67-2.710.267700.201656726
2.71-2.760.245760.213669745
2.76-2.810.219690.21661730
2.81-2.870.226740.22653727
2.87-2.920.284710.211675746
2.92-2.990.247750.204673748
2.99-3.060.266590.203690749
3.06-3.130.26880.199679767
3.13-3.220.268590.208696755
3.22-3.310.233720.199688760
3.31-3.420.203700.206695765
3.42-3.540.201980.189661759
3.54-3.680.179860.18673759
3.68-3.850.188750.184698773
3.85-4.050.144720.162696768
4.05-4.310.187730.169702775
4.31-4.640.161670.161698765
4.64-5.110.193730.178725798
5.11-5.850.265760.202720796
5.85-7.360.284760.227743819
7.36-500.209800.235794874
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3mol.par

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