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- PDB-3kfq: Unreduced cathepsin V in complex with stefin A -

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Basic information

Entry
Database: PDB / ID: 3kfq
TitleUnreduced cathepsin V in complex with stefin A
Components
  • Cathepsin L2
  • Cystatin-A
KeywordsHydrolase/Hydrolase inhibitor / papain-like cysteine protease / cathepsin / protease-inhibitor complex / Hydrolase / Lysosome / Protease / Thiol protease / Zymogen / Protease inhibitor / Thiol protease inhibitor / Hydrolase-Hydrolase inhibitor complex
Function / homology
Function and homology information


cathepsin V / peptidase inhibitor complex / peptide cross-linking / Formation of the cornified envelope / cornified envelope / 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 / extracellular matrix disassembly ...cathepsin V / peptidase inhibitor complex / peptide cross-linking / Formation of the cornified envelope / cornified envelope / 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 / extracellular matrix disassembly / cysteine-type endopeptidase inhibitor activity / keratinocyte differentiation / Degradation of the extracellular matrix / negative regulation of proteolysis / MHC class II antigen presentation / cysteine-type peptidase activity / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / cell-cell adhesion / antigen processing and presentation of exogenous peptide antigen via MHC class II / protease binding / lysosome / serine-type endopeptidase activity / cysteine-type endopeptidase activity / extracellular space / extracellular region / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
Proteinase inhibitor I25A, stefin / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) ...Proteinase inhibitor I25A, stefin / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / 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 / Nuclear Transport Factor 2; Chain: A, / Papain-like cysteine peptidase superfamily / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Cathepsin L2 / Cystatin-A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsRenko, M. / Turk, D.
CitationJournal: To be Published
Title: Unreduced cathepsin V in complex with stefin A
Authors: Renko, M. / Turk, D.
History
DepositionOct 27, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cathepsin L2
B: Cathepsin L2
C: Cystatin-A
D: Cystatin-A


Theoretical massNumber of molelcules
Total (without water)70,2154
Polymers70,2154
Non-polymers00
Water13,007722
1
A: Cathepsin L2
D: Cystatin-A


Theoretical massNumber of molelcules
Total (without water)35,1082
Polymers35,1082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-12 kcal/mol
Surface area14090 Å2
MethodPISA
2
B: Cathepsin L2
C: Cystatin-A


Theoretical massNumber of molelcules
Total (without water)35,1082
Polymers35,1082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-12 kcal/mol
Surface area14240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.313, 107.290, 115.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cathepsin L2 / Cathepsin V / Cathepsin U


Mass: 24087.053 Da / Num. of mol.: 2 / Mutation: N108Q,N179D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: O60911, cathepsin V
#2: Protein Cystatin-A / Cystatin-AS / Stefin-A


Mass: 11020.464 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pet3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01040
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 722 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCATHEPSIN V WAS BLOCKED WITH MMTS (METHYL METHANETHIOSULFONATE), LEAVING -S-CH3 ATOMS ON ACTIVE ...CATHEPSIN V WAS BLOCKED WITH MMTS (METHYL METHANETHIOSULFONATE), LEAVING -S-CH3 ATOMS ON ACTIVE SITE CYSTEINE RESIDUE.

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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: 2.63 Å3/Da / Density % sol: 53.19 % / Mosaicity: 0.546 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris-HCl, 12% PEG3000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 15, 2008 / Details: Collimating and focusing, Pt-coated mirrors
RadiationMonochromator: Double Crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→22 Å / Num. all: 51300 / Num. obs: 51049 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.2 % / Rmerge(I) obs: 0.079 / Χ2: 0.88 / Net I/σ(I): 8
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.43 / Num. unique all: 2302 / Χ2: 0.462 / % possible all: 91.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3h6s, 1nb3

3h6s

1nb3


Resolution: 1.99→19.49 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.164 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.867 / SU R Cruickshank DPI: 0.166 / SU Rfree: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY. The structure was refined also with MAIN
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2586 5.1 %RANDOM
Rwork0.176 ---
all0.182 51180 --
obs0.178 50986 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 81.22 Å2 / Biso mean: 32.922 Å2 / Biso min: 13.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å2-0 Å2-0 Å2
2---1.21 Å20 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.99→19.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4932 0 0 722 5654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225010
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.9516783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5555634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.79325.566221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57815832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2931512
X-RAY DIFFRACTIONr_chiral_restr0.1280.2714
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213846
X-RAY DIFFRACTIONr_mcbond_it0.9161.53156
X-RAY DIFFRACTIONr_mcangle_it1.60725055
X-RAY DIFFRACTIONr_scbond_it2.61531854
X-RAY DIFFRACTIONr_scangle_it4.1234.51728
LS refinement shellResolution: 1.995→2.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 169 -
Rwork0.22 3443 -
all-3612 -
obs--96.97 %

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