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- PDB-3h8b: A combined crystallographic and molecular dynamics study of cathe... -

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Basic information

Entry
Database: PDB / ID: 3h8b
TitleA combined crystallographic and molecular dynamics study of cathepsin-L retro-binding inhibitors(compound 9)
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 / Trafficking and processing of endosomal TLR / proteoglycan binding / zymogen activation / Assembly of collagen fibrils and other multimeric structures / antigen processing and presentation / protein autoprocessing / Collagen degradation / collagen catabolic process / fibronectin binding / serpin family protein binding / collagen binding / Attachment and Entry / Degradation of the extracellular matrix / receptor-mediated endocytosis of virus by host cell / multivesicular body / endocytic vesicle lumen / MHC class II antigen presentation / cysteine-type peptidase activity / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / : / histone binding / adaptive immune response / Attachment and Entry / lysosome / 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 / symbiont entry into host cell / 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-NSY / Procathepsin L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)150,79712
Polymers145,1506
Non-polymers5,6476
Water10,124562
1
A: Cathepsin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1332
Polymers24,1921
Non-polymers9411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cathepsin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1332
Polymers24,1921
Non-polymers9411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cathepsin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1332
Polymers24,1921
Non-polymers9411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cathepsin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1332
Polymers24,1921
Non-polymers9411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Cathepsin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1332
Polymers24,1921
Non-polymers9411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Cathepsin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1332
Polymers24,1921
Non-polymers9411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.990, 99.234, 206.462
Angle α, β, γ (deg.)90.00, 90.05, 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: Cathepsin L / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P07711, cathepsin L
#2: Chemical
ChemComp-NSY / N~2~,N~6~-bis(biphenyl-4-ylacetyl)-L-lysyl-D-arginyl-N-(2-phenylethyl)-L-phenylalaninamide


Mass: 941.169 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C57H64N8O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.19 Å3/Da / Density % sol: 43.77 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 116974 / Rsym value: 0.06 / Net I/σ(I): 17.1

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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: 1.8→45 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 3874
RfactorNum. reflection% reflectionSelection details
Rfree0.25 8770 7.6 %RANDOM
Rwork0.216 100135 --
obs-108905 94.2 %-
Solvent computationBsol: 40.919 Å2
Displacement parametersBiso max: 101.66 Å2 / Biso mean: 27.671 Å2 / Biso min: 8.22 Å2
Baniso -1Baniso -2Baniso -3
1--3.267 Å20 Å2-0.218 Å2
2---1.835 Å20 Å2
3---5.102 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9953 0 420 562 10935
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_d1.34

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