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- PDB-2xu3: CATHEPSIN L WITH A NITRILE INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 2xu3
TitleCATHEPSIN L WITH A NITRILE INHIBITOR
ComponentsCATHEPSIN L1
KeywordsHYDROLASE / DRUG DESIGN / THIOL PROTEASE
Function / homology
Function and homology information


enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus ...enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus / zymogen activation / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / cysteine-type endopeptidase activator activity involved in apoptotic process / antigen processing and presentation / protein autoprocessing / Collagen degradation / fibronectin binding / collagen catabolic process / serpin family protein binding / cysteine-type peptidase activity / endocytic vesicle lumen / Attachment and Entry / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / multivesicular body / 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 / histone binding / collagen-containing extracellular matrix / adaptive immune response / receptor-mediated endocytosis of virus by host cell / lysosome / Attachment and Entry / immune response / symbiont entry into host cell / apical plasma membrane / cysteine-type endopeptidase activity / fusion of virus membrane with host plasma membrane / intracellular membrane-bounded organelle / fusion of virus membrane with host endosome membrane / Golgi apparatus / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus / plasma 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-XU3 / Procathepsin L
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å
AuthorsBanner, D.W. / Benz, J.M. / Haap, W.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2011
Title: Systematic Investigation of Halogen Bonding in Protein-Ligand Interactions.
Authors: Hardegger, L.A. / Kuhn, B. / Spinnler, B. / Anselm, L. / Ecabert, R. / Stihle, M. / Gsell, B. / Thoma, R. / Diez, J. / Benz, J. / Plancher, J.M. / Hartmann, G. / Banner, D.W. / Haap, W. / Diederich, F.
History
DepositionOct 14, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 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 L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1865
Polymers24,1921
Non-polymers9944
Water6,720373
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.441, 49.394, 46.129
Angle α, β, γ (deg.)90.00, 105.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CATHEPSIN L1 / MAJOR EXCRETED PROTEIN / MEP


Mass: 24191.701 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 114-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P07711, cathepsin L
#2: Chemical ChemComp-XU3 / (2S,4R)-4-(2-chlorophenyl)sulfonyl-1-[1-(5-chlorothiophen-2-yl)cyclopropyl]carbonyl-N-[1-(iminomethyl)cyclopropyl]pyrrolidine-2-carboxamide


Mass: 540.482 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H23Cl2N3O4S2
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsORIGINAL COMPOUND (2S,4R)-4-(2-CHLORO-BENZENESULFONYL)-1-[1- (5-CHLORO-THIOPHEN-2-YL)- ...ORIGINAL COMPOUND (2S,4R)-4-(2-CHLORO-BENZENESULFONYL)-1-[1- (5-CHLORO-THIOPHEN-2-YL)-CYCLOPROPANECARBONYL-PYRROLIDINE-2- CARBOXYLIC ACID (1-CYANO-CYCLOPROPYL)-AMIDE REACTS WITH CYS TO BECOME XU3 VIA REDUCTION OF THE TRIPLE BOND

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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: 1.93 Å3/Da / Density % sol: 36.6 % / Description: NONE
Crystal growpH: 8.2 / Details: 0.1 M CITRIC ACID PH 3.5 25 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.7
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 0.9→50 Å / Num. obs: 139614 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 3.32 % / Biso Wilson estimate: 9.15 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.11
Reflection shellResolution: 0.9→1 Å / Redundancy: 3.19 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.25 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0077refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HWN

3hwn


Resolution: 0.9→44.53 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.593 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS GENERATED AT RIDING POSITIONS BY REFMAC. ZERO OCCUPANCY HYDROGENS REMOVED.
RfactorNum. reflection% reflectionSelection details
Rfree0.15473 6706 5.1 %RANDOM
Rwork0.14183 ---
obs0.14248 125923 93.19 %-
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: 8.362 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20.19 Å2
2--0.07 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 0.9→44.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 63 373 2133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212022
X-RAY DIFFRACTIONr_bond_other_d0.0010.021345
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9942776
X-RAY DIFFRACTIONr_angle_other_deg0.87833290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9145256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09725.41796
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.06715309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.323157
X-RAY DIFFRACTIONr_chiral_restr0.1010.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022370
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02414
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_restr4.62611440
X-RAY DIFFRACTIONr_sphericity_free7.9635374
X-RAY DIFFRACTIONr_sphericity_bonded2.93853295
LS refinement shellResolution: 0.9→0.923 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 408 -
Rwork0.367 8273 -
obs--82.62 %

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