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- PDB-1the: CRYSTAL STRUCTURES OF RECOMBINANT RAT CATHEPSIN B AND A CATHEPSIN... -

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Basic information

Entry
Database: PDB / ID: 1the
TitleCRYSTAL STRUCTURES OF RECOMBINANT RAT CATHEPSIN B AND A CATHEPSIN B-INHIBITOR COMPLEX: IMPLICATIONS FOR STRUCTURE-BASED INHIBITOR DESIGN
ComponentsCathepsin B
KeywordsHYDROLASE/HYDROLASE INHIBITOR / THIOL PROTEASE / Glycoprotein / Protease / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Trafficking and processing of endosomal TLR / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / kininogen binding / cathepsin B / response to interleukin-4 / peptidase inhibitor complex / MHC class II antigen presentation / response to kainic acid / thyroid hormone generation ...Trafficking and processing of endosomal TLR / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / kininogen binding / cathepsin B / response to interleukin-4 / peptidase inhibitor complex / MHC class II antigen presentation / response to kainic acid / thyroid hormone generation / cellular response to thyroid hormone stimulus / proteoglycan binding / Neutrophil degranulation / response to dexamethasone / response to amine / decidualization / collagen catabolic process / response to mechanical stimulus / response to glucose / skeletal muscle tissue development / collagen binding / response to cytokine / epithelial cell differentiation / peptide binding / cysteine-type peptidase activity / proteolysis involved in protein catabolic process / protein catabolic process / cellular response to mechanical stimulus / response to peptide hormone / sarcolemma / caveola / autophagy / melanosome / peptidase activity / neuron apoptotic process / response to ethanol / spermatogenesis / endopeptidase activity / lysosome / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / symbiont entry into host cell / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / proteolysis / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Peptidase C1A, propeptide / Peptidase family C1 propeptide / 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 ...Peptidase C1A, propeptide / Peptidase family C1 propeptide / 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
amino{[(4R)-4-{[(benzyloxy)carbonyl]amino}-5-({(1R)-1-[(benzyloxy)methyl]-3-chloro-2-oxopropyl}amino)-5- oxopentyl]amino}methaniminium / Chem-0E6 / Cathepsin B
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsHuber, C.P. / Jia, Z.
Citation
Journal: J.Biol.Chem. / Year: 1995
Title: Crystal structures of recombinant rat cathepsin B and a cathepsin B-inhibitor complex. Implications for structure-based inhibitor design.
Authors: Jia, Z. / Hasnain, S. / Hirama, T. / Lee, X. / Mort, J.S. / To, R. / Huber, C.P.
#1: Journal: J.Biol.Chem. / Year: 1990
Title: Crystallization of Recombinant Rat Cathepsin B
Authors: Lee, X. / Ahmed, F.R. / Hirama, T. / Huber, C.P. / Rose, D.R. / To, R. / Hasnain, S. / Tam, A. / Mort, J.S.
History
DepositionSep 15, 1995Processing site: BNL
Revision 1.0Mar 10, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700SHEET THERE IS A BIFURCATED SHEET IN EACH CHAIN OF THIS ENTRY. A BIFURCATED SHEET IS PRESENTED AS ...SHEET THERE IS A BIFURCATED SHEET IN EACH CHAIN OF THIS ENTRY. A BIFURCATED SHEET IS PRESENTED AS TWO SHEETS WITH ONE OR MORE STRANDS IN COMMON.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cathepsin B
B: Cathepsin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9214
Polymers56,8832
Non-polymers1,0382
Water4,288238
1
A: Cathepsin B
hetero molecules

B: Cathepsin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9214
Polymers56,8832
Non-polymers1,0382
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area2240 Å2
ΔGint-12 kcal/mol
Surface area19750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.110, 90.150, 62.310
Angle α, β, γ (deg.)90.00, 97.24, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.6405, 0.7349, 0.2229), (0.7354, -0.6706, 0.0975), (0.2211, 0.1015, -0.97)
Vector: -52.354, 88.605, 94.504)

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Components

#1: Protein Cathepsin B / Cathepsin B1 / RSG-2 / Cathepsin B light chain / Cathepsin B heavy chain


Mass: 28441.562 Da / Num. of mol.: 2 / Mutation: S115A
Source method: isolated from a genetically manipulated source
Details: RECOMBINANT RAT ENZYME / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: CDNA, Ctsb / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00787, cathepsin B
#2: Chemical ChemComp-0E6 / amino{[(4S)-4-{[(benzyloxy)carbonyl]amino}-5-{[(2S)-1-(benzyloxy)-4-chloro-3-oxobutan-2-yl]amino}-5-oxopentyl]amino}met haniminium / benzyloxycarbonyl-Arg-Ser(O-Bzl) chloromethylketone


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 519.013 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H33ClN5O5
References: amino{[(4R)-4-{[(benzyloxy)carbonyl]amino}-5-({(1R)-1-[(benzyloxy)methyl]-3-chloro-2-oxopropyl}amino)-5- oxopentyl]amino}methaniminium
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE VAL 223 ALA SUBSTITUTION WAS PRESENT IN THE PLASMID SUPPLIED TO DR. J. S. MORT BY DR. SHU CHAN ...THE VAL 223 ALA SUBSTITUTION WAS PRESENT IN THE PLASMID SUPPLIED TO DR. J. S. MORT BY DR. SHU CHAN ALTHOUGH IT IS NOT MENTIONED IN THE PAPER GIVING THE CDNA SEQUENCE. IT IS POSSIBLE THAT THIS CHANGE, ALSO WITH RESPECT TO THE ORIGINAL PROTEIN SEQUENCE FROM A PREPARATION OF PURIFIED PROTEIN, COULD REPRESENT A POLYMORPHISM BETWEEN THE STRAINS OF RAT THAT WERE USED IN EACH CASE. THE SUBSTITUTION IS NOT STRUCTURALLY IMPORTANT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMphosphate1drop
20.001 %Brij-351drop
30.05 %1dropNaN3
47.7 mg/mlprotein1drop
510 %PEG80001reservoir
60.2 Mammonium sulfate1reservoir
70.1 Msodium citrate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Sep 1, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→14.3 Å / Num. obs: 39749 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
SDMSdata collection
X-PLOR3model building
X-PLOR3refinement
SDMSdata reduction
X-PLOR3phasing
RefinementResolution: 1.9→8 Å / σ(F): 2
Details: RESIDUE ASN 222 OF BOTH CHAINS HAS PHI-PSI ANGLES OUTSIDE THE NORMALLY PERMITTED RANGE BECAUSE ITS SIDECHAIN OXYGEN ATOM IS INVOLVED IN A HYDROGEN BOND WITH THE ADJACENT MAIN-CHAIN N-H 223.
RfactorNum. reflection% reflection
Rwork0.17 --
obs0.17 37830 96.3 %
Displacement parametersBiso mean: 19.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3862 0 70 238 4170
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.59
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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