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- PDB-4mzo: Mouse cathepsin s with covalent ligand (3S,4S)-N-[(2E)-2-IMINOETH... -

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Basic information

Entry
Database: PDB / ID: 4mzo
TitleMouse cathepsin s with covalent ligand (3S,4S)-N-[(2E)-2-IMINOETHYL]-4-(MORPHOLIN-4-YLCARBONYL)-1-(PHENYLSULFONYL)PYRROLIDINE-3-CARBOXAMIDE
ComponentsCathepsin S
Keywordshydrolase/hydrolase inhibitor / HYDROLASE / CYSTEINE PROTEASE / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


Assembly of collagen fibrils and other multimeric structures / Trafficking and processing of endosomal TLR / cathepsin S / basement membrane disassembly / Degradation of the extracellular matrix / positive regulation of cation channel activity / MHC class II antigen presentation / cysteine-type endopeptidase activator activity involved in apoptotic process / bone resorption / phagocytic vesicle ...Assembly of collagen fibrils and other multimeric structures / Trafficking and processing of endosomal TLR / cathepsin S / basement membrane disassembly / Degradation of the extracellular matrix / positive regulation of cation channel activity / MHC class II antigen presentation / cysteine-type endopeptidase activator activity involved in apoptotic process / bone resorption / phagocytic vesicle / cysteine-type peptidase activity / Neutrophil degranulation / early endosome lumen / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / positive regulation of inflammatory response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptidase activity / lysosome / immune response / cysteine-type endopeptidase activity / cell surface / proteolysis / extracellular space / 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
Chem-2EW / Cathepsin S
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsKuglstatter, A. / Stihle, M.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Identification of potent and selective cathepsin S inhibitors containing different central cyclic scaffolds.
Authors: Hilpert, H. / Mauser, H. / Humm, R. / Anselm, L. / Kuehne, H. / Hartmann, G. / Gruener, S. / Banner, D.W. / Benz, J. / Gsell, B. / Kuglstatter, A. / Stihle, M. / Thoma, R. / Sanchez, R.A. / ...Authors: Hilpert, H. / Mauser, H. / Humm, R. / Anselm, L. / Kuehne, H. / Hartmann, G. / Gruener, S. / Banner, D.W. / Benz, J. / Gsell, B. / Kuglstatter, A. / Stihle, M. / Thoma, R. / Sanchez, R.A. / Iding, H. / Wirz, B. / Haap, W.
History
DepositionSep 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
C: Cathepsin S
D: Cathepsin S
E: Cathepsin S
F: Cathepsin S
G: Cathepsin S
H: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,56816
Polymers197,3008
Non-polymers3,2688
Water13,944774
1
A: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0712
Polymers24,6621
Non-polymers4081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0712
Polymers24,6621
Non-polymers4081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0712
Polymers24,6621
Non-polymers4081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0712
Polymers24,6621
Non-polymers4081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0712
Polymers24,6621
Non-polymers4081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0712
Polymers24,6621
Non-polymers4081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0712
Polymers24,6621
Non-polymers4081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0712
Polymers24,6621
Non-polymers4081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.205, 86.063, 119.320
Angle α, β, γ (deg.)90.00, 90.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cathepsin S


Mass: 24662.480 Da / Num. of mol.: 8 / Fragment: RESIDUES 116-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ctss, Cats / Production host: Escherichia coli (E. coli) / References: UniProt: O70370, cathepsin S
#2: Chemical
ChemComp-2EW / (3S,4S)-N-[(2E)-2-iminoethyl]-4-(morpholin-4-ylcarbonyl)-1-(phenylsulfonyl)pyrrolidine-3-carboxamide


Mass: 408.472 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C18H24N4O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 774 / 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: 1.91 Å3/Da / Density % sol: 35.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 3350, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.703
11-h,-k,l20.297
ReflectionResolution: 1.47→49.03 Å / Num. obs: 234207 / % possible obs: 94.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.5
Reflection shellResolution: 1.47→1.55 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 0.9 / Num. unique all: 29202 / % possible all: 80.6

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BS5

4bs5


Resolution: 1.47→49.03 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.917 / SU B: 1.082 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27473 11792 5 %RANDOM
Rwork0.23078 ---
obs0.233 222353 92.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.144 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20 Å21.45 Å2
2---4.56 Å2-0 Å2
3---2.88 Å2
Refinement stepCycle: LAST / Resolution: 1.47→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13366 0 224 774 14364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.01914020
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.7161.95719013
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.60551760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77624.929635
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.718152190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5941540
X-RAY DIFFRACTIONr_chiral_restr0.1790.21921
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.02110866
X-RAY DIFFRACTIONr_gen_planes_other
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
LS refinement shellResolution: 1.466→1.504 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.46 465 -
Rwork0.311 8691 -
obs--49.12 %

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