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- PDB-1fh0: CRYSTAL STRUCTURE OF HUMAN CATHEPSIN V COMPLEXED WITH AN IRREVERS... -

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Basic information

Entry
Database: PDB / ID: 1fh0
TitleCRYSTAL STRUCTURE OF HUMAN CATHEPSIN V COMPLEXED WITH AN IRREVERSIBLE VINYL SULFONE INHIBITOR
ComponentsCATHEPSIN V
KeywordsHYDROLASE/HYDROLASE inhibitor / cathepsin / papain / protease / cancer / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


cathepsin V / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / Trafficking and processing of endosomal TLR / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / cysteine-type endopeptidase activator activity involved in apoptotic process / extracellular matrix disassembly / Degradation of the extracellular matrix / MHC class II antigen presentation / cysteine-type peptidase activity ...cathepsin V / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / Trafficking and processing of endosomal TLR / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / cysteine-type endopeptidase activator activity involved in apoptotic process / extracellular matrix disassembly / Degradation of the extracellular matrix / MHC class II antigen presentation / cysteine-type peptidase activity / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / positive regulation of apoptotic signaling pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / immune response / cysteine-type endopeptidase activity / serine-type endopeptidase activity / 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 peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
MePip-Phe-HphVSPh / Chem-0IW / Cathepsin L2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsSomoza, J.R.
CitationJournal: Biochemistry / Year: 2000
Title: Crystal structure of human cathepsin V.
Authors: Somoza, J.R. / Zhan, H. / Bowman, K.K. / Yu, L. / Mortara, K.D. / Palmer, J.T. / Clark, J.M. / McGrath, M.E.
History
DepositionJul 30, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Oct 12, 2011Group: Non-polymer description
Revision 1.4Feb 27, 2013Group: Other
Revision 1.5Oct 4, 2017Group: Refinement description / Category: software
Revision 1.6Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Mar 13, 2024Group: Data collection / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity / pdbx_entity_src_syn
Item: _entity.details
Revision 1.8Nov 20, 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

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Assembly

Deposited unit
A: CATHEPSIN V
B: CATHEPSIN V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3315
Polymers48,0822
Non-polymers1,2503
Water5,170287
1
A: CATHEPSIN V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7143
Polymers24,0411
Non-polymers6732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CATHEPSIN V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6182
Polymers24,0411
Non-polymers5771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.7, 104.7, 179.2
Angle α, β, γ (deg.)90, 90, 120
Int Tables number181
Space group name H-MP6422
DetailsThis enzyme is most likely active as a monomer.

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Components

#1: Protein CATHEPSIN V / CATHEPSIN L2


Mass: 24040.959 Da / Num. of mol.: 2 / Mutation: N108Q, N178D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: O60911, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-0IW / Nalpha-[(4-methylpiperazin-1-yl)carbonyl]-N-[(3S)-1-phenyl-5-(phenylsulfonyl)pentan-3-yl]-L-phenylalaninamide / APC-3316, bound form / 4-Methylpiperazine-1-carboxylic acid [1-[(3-benzenesulfonyl-1-phenethylallyl)carbamoyl]-2-phenylethyl]amide, bound form


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 576.749 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H40N4O4S
Details: This inhibitor is covalently linked to BNS, 4-SULFONYLBENZENE GROUP, to form an irreversible vinyl sulfone inhibitor.
References: MePip-Phe-HphVSPh
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsINHIBITOR 4-METHYLPIPERAZINE-1-CARBOXYLIC ACID [1-[(3-BENZENESULFONYL-1-PHENETHYLALLYL)CARBAMOYL]-2- ...INHIBITOR 4-METHYLPIPERAZINE-1-CARBOXYLIC ACID [1-[(3-BENZENESULFONYL-1-PHENETHYLALLYL)CARBAMOYL]-2-PHENYLETHYL]AMIDE WAS USED FOR CRYSTALLIZATION. THE C11-C21 SINGLE BOND IN 0IW IS GENERATED AS A RESULT OF REACTION OF THE CYS 25 THIOL WITH THE OLEFINIC DOUBLE BOND OF THE INHIBIOR

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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: 2.9 Å3/Da / Density % sol: 57.54 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Lithium sulfate, PEG 4000, tris, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 4.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.17 Mlithium sulfate1reservoir
20.085 MTris1reservoir
325.5 %(w/v)PEG40001reservoir
415 %(v/v)glycerol1reservoir
512 mg/mlprotein1drop
625 mMsodium acetate1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 22, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.6→100 Å / Num. all: 78054 / Num. obs: 78054 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 37.3
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 5 % / Rmerge(I) obs: 0.424 / Num. unique all: 3539 / % possible all: 89.9
Reflection
*PLUS
Highest resolution: 1.6 Å / Num. measured all: 386837
Reflection shell
*PLUS
Highest resolution: 1.6 Å / % possible obs: 89.9 % / Mean I/σ(I) obs: 3.45

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Processing

Software
NameClassification
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNXrefinement
RefinementResolution: 1.6→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.211 7386 -random
Rwork0.197 ---
all0.198 73072 --
obs0.198 73072 95 %-
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3378 0 87 287 3752
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.18
Software
*PLUS
Name: CNX / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 50 Å / σ(F): 0 / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg

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