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- PDB-2xu1: CATHEPSIN L WITH A NITRILE INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 2xu1
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 / protein autoprocessing / Collagen degradation / fibronectin binding / antigen processing and presentation / collagen catabolic process / serpin family protein binding / cysteine-type peptidase activity / Attachment and Entry / positive regulation of apoptotic signaling pathway / endocytic vesicle lumen / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / multivesicular body / proteolysis involved in protein catabolic process / lysosomal lumen / Endosomal/Vacuolar pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / histone binding / collagen-containing extracellular matrix / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / adaptive immune response / lysosome / immune response / symbiont entry into host cell / apical plasma membrane / fusion of virus membrane with host plasma membrane / cysteine-type endopeptidase activity / 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-424 / Procathepsin L
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.45 Å
AuthorsBanner, D.W. / Benz, J.M. / Steinbacher, S. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CATHEPSIN L1
B: CATHEPSIN L1
C: CATHEPSIN L1
D: CATHEPSIN L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,7858
Polymers96,6474
Non-polymers2,1384
Water12,971720
1
A: CATHEPSIN L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6962
Polymers24,1621
Non-polymers5341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CATHEPSIN L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6962
Polymers24,1621
Non-polymers5341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CATHEPSIN L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6962
Polymers24,1621
Non-polymers5341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: CATHEPSIN L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6962
Polymers24,1621
Non-polymers5341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.360, 62.705, 68.243
Angle α, β, γ (deg.)105.62, 93.24, 115.45
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 24161.676 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN, RESIDUES 114-333 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P07711, cathepsin L
#2: Chemical
ChemComp-424 / (2S,4R)-1-[1-(4-chlorophenyl)cyclopropyl]carbonyl-4-(2-chlorophenyl)sulfonyl-N-[1-(iminomethyl)cyclopropyl]pyrrolidine-2-carboxamide


Mass: 534.455 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H25Cl2N3O4S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 720 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPROTEIN WAS CRYSTALLIZED AFTER TREATMENT WITH (2S, 4R)-4-(2-CHLORO-BENZENESULFONYL)-1-[1-(4-CHLORO- ...PROTEIN WAS CRYSTALLIZED AFTER TREATMENT WITH (2S, 4R)-4-(2-CHLORO-BENZENESULFONYL)-1-[1-(4-CHLORO-PHENYL) -CYCLOPROPANECARBONYL]-PYRROLIDINE-2-CARBOXYLIC ACID (1-CYANO- CYCLOPROPYL)-AMIDE. LIGAND WITH RESIDUE NAME 424 DERIVES FROM THIS.
Sequence detailsTHR110 TO ALA MUTANT (T110A) CORRESPONDING TO RESIDUE 223 IN THE UNIPROT NUMBERING.

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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: 2.14 Å3/Da / Density % sol: 42.5 % / Description: ISOMORPHOUS TO PDB ENTRY 3HWN
Crystal growpH: 4 / Details: 20% PEG 2000, PH 4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.008
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 137183 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 2.28 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 5.79
Reflection shellResolution: 1.45→1.55 Å / Redundancy: 2.29 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.46 / % possible all: 93.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0041refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.45→36.52 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.891 / SU B: 2.292 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27217 4452 3.6 %RANDOM
Rwork0.23367 ---
obs0.23504 120732 87.09 %-
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: 11.311 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.1 Å20.1 Å2
2---0.13 Å2-0.65 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.45→36.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6695 0 140 720 7555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227185
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.9649776
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6115900
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.04325.102343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.472151121
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9291526
X-RAY DIFFRACTIONr_chiral_restr0.0950.2965
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215674
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_it0.0160.246678
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: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 292 -
Rwork0.324 7602 -
obs--74.25 %

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