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- PDB-3h89: A combined crystallographic and molecular dynamics study of cathe... -

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Basic information

Entry
Database: PDB / ID: 3h89
TitleA combined crystallographic and molecular dynamics study of cathepsin-L retro-binding inhibitors(compound 4)
ComponentsCathepsin L1
KeywordsHYDROLASE / Cysteine proteases / Cathepsin L / Disulfide bond / Glycoprotein / Lysosome / Protease / Thiol protease / Zymogen
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 / fibronectin binding / Collagen degradation / antigen processing and presentation / collagen catabolic process / serpin family protein binding / Attachment and Entry / cysteine-type peptidase activity / endocytic vesicle lumen / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / multivesicular body / lysosomal lumen / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / Endosomal/Vacuolar 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 / Attachment and Entry / lysosome / symbiont entry into host cell / immune response / 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-NSX / Procathepsin L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTulsidas, S.R. / Chowdhury, S.F. / Kumar, S. / Joseph, L. / Purisima, E.O. / Sivaraman, J.
CitationJournal: J.Med.Chem. / Year: 2009
Title: A combined crystallographic and molecular dynamics study of cathepsin L retrobinding inhibitors
Authors: Shenoy, R.T. / Chowdhury, S.F. / Kumar, S. / Joseph, L. / Purisima, E.O. / Sivaraman, J.
History
DepositionApr 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2014Group: Database references

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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
E: Cathepsin L1
F: Cathepsin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,89312
Polymers145,1506
Non-polymers5,7436
Water4,071226
1
A: Cathepsin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1492
Polymers24,1921
Non-polymers9571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cathepsin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1492
Polymers24,1921
Non-polymers9571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cathepsin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1492
Polymers24,1921
Non-polymers9571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cathepsin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1492
Polymers24,1921
Non-polymers9571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Cathepsin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1492
Polymers24,1921
Non-polymers9571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Cathepsin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1492
Polymers24,1921
Non-polymers9571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.404, 61.075, 205.184
Angle α, β, γ (deg.)90.00, 89.91, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Cathepsin L1 / / Major excreted protein / MEP / Cathepsin L1 heavy chain / Cathepsin L1 light chain


Mass: 24191.701 Da / Num. of mol.: 6
Fragment: Cathepsin L Heavy Chain and Light Chain, UNP residues 114-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Catehpsin L / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07711, cathepsin L
#2: Chemical
ChemComp-NSX / N~2~,N~6~-bis(biphenyl-4-ylacetyl)-L-lysyl-D-arginyl-N-(2-phenylethyl)-L-tyrosinamide


Mass: 957.168 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C57H64N8O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.67 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.43→50 Å / Num. obs: 42927 / Rsym value: 0.048 / Net I/σ(I): 22.2

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Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→25 Å / Cross valid method: THROUGHOUT / σ(F): 1629
RfactorNum. reflection% reflectionSelection details
Rfree0.28 3002 7 %RANDOM
Rwork0.22 34041 --
obs-37043 86.1 %-
Solvent computationksol: 34.837 e/Å3
Displacement parametersBiso max: 110.15 Å2 / Biso mean: 28.415 Å2 / Biso min: 1.6 Å2
Baniso -2Baniso -3
1-0 Å20 Å2
2--5.333 Å20 Å2
3--5.59 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9954 0 426 226 10606
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.293

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