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- PDB-4bpv: MOUSE CATHEPSIN S WITH COVALENT LIGAND -

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Basic information

Entry
Database: PDB / ID: 4bpv
TitleMOUSE CATHEPSIN S WITH COVALENT LIGAND
ComponentsCATHEPSIN S
KeywordsHYDROLASE / CYSTEINE PROTEASE / COVALENT LIGAND
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-OFH / Cathepsin S
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBanner, D.W. / Benz, J. / Gsell, B. / Stihle, M. / Ruf, A. / Haap, W.
CitationJournal: To be Published
Title: Cathepsin S Nitrile Inhibitors
Authors: Haap, W. / Banner, D.W.
History
DepositionMay 28, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
K: CATHEPSIN S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,99511
Polymers147,9756
Non-polymers3,0205
Water16,898938
1
A: CATHEPSIN S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2662
Polymers24,6621
Non-polymers6041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CATHEPSIN S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2662
Polymers24,6621
Non-polymers6041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CATHEPSIN S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2662
Polymers24,6621
Non-polymers6041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: CATHEPSIN S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2662
Polymers24,6621
Non-polymers6041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: CATHEPSIN S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2662
Polymers24,6621
Non-polymers6041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
K: CATHEPSIN S


Theoretical massNumber of molelcules
Total (without water)24,6621
Polymers24,6621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.855, 128.917, 97.132
Angle α, β, γ (deg.)90.00, 97.44, 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.: 6 / Fragment: RESIDUES 116-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O70370, cathepsin S
#2: Chemical
ChemComp-OFH / (4R)-4-[(2-chloro-4-{[(2S)-1,1,1-trifluoropropan-2-yl]oxy}phenyl)sulfonyl]-N-{1-[(E)-iminomethyl]cyclopropyl}-1-{[1-(trifluoromethyl)cyclopropyl]carbonyl}-L-prolinamide


Mass: 603.962 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C23H24ClF6N3O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 938 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence details116-340 NO MUTATIONS

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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: 3.45 Å3/Da / Density % sol: 64.4 % / Description: NONE
Crystal growpH: 7.5 / Details: 25% PEG 3350, 0.1 M HEPES PH7.5, 0.2M NH4AC

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→45.1 Å / Num. obs: 128672 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.78 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.33
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.52 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.84 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN HOUSE STRUCTURES

Resolution: 2→45.11 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.906 / SU B: 4.487 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS BUT NOT OUTPUT. U VALUES REFINED INDIVIDUALLY. CHAINS A,B,C,D FORM LAYERS. E BRIDGES THE LAYERS AND K IS ONLY PARTIALLY VISIBLE
RfactorNum. reflection% reflectionSelection details
Rfree0.25537 5904 5 %RANDOM
Rwork0.21225 ---
obs0.2144 111339 97.8 %-
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: 33.644 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.06 Å2
2---0.04 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2→45.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9065 0 195 938 10198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0199596
X-RAY DIFFRACTIONr_bond_other_d0.0020.028552
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.96513051
X-RAY DIFFRACTIONr_angle_other_deg0.9673.00419714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.87451195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26924.897435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.774151487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3211528
X-RAY DIFFRACTIONr_chiral_restr0.0960.21336
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211150
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022258
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: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 389 -
Rwork0.332 7831 -
obs--93.29 %

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