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

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Basic information

Entry
Database: PDB / ID: 1cte
TitleCRYSTAL STRUCTURES OF RECOMBINANT RAT CATHEPSIN B AND A CATHEPSIN B-INHIBITOR COMPLEX: IMPLICATIONS FOR STRUCTURE-BASED INHIBITOR DESIGN
ComponentsCATHEPSIN BCathepsin
KeywordsTHIOL PROTEASE
Function / homology
Function and homology information


Trafficking and processing of endosomal TLR / Assembly of collagen fibrils and other multimeric structures / kininogen binding / cathepsin B / Collagen degradation / response to interleukin-4 / peptidase inhibitor complex / MHC class II antigen presentation / thyroid hormone generation / cellular response to thyroid hormone stimulus ...Trafficking and processing of endosomal TLR / Assembly of collagen fibrils and other multimeric structures / kininogen binding / cathepsin B / Collagen degradation / response to interleukin-4 / peptidase inhibitor complex / MHC class II antigen presentation / 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 glucose / response to mechanical stimulus / skeletal muscle tissue development / cysteine-type peptidase activity / epithelial cell differentiation / collagen binding / proteolysis involved in protein catabolic process / response to cytokine / peptide binding / protein catabolic process / response to organic cyclic compound / sarcolemma / response to peptide hormone / autophagy / cellular response to mechanical stimulus / : / melanosome / peptidase activity / spermatogenesis / neuron apoptotic process / response to ethanol / endopeptidase activity / lysosome / symbiont entry into host cell / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / proteolysis / extracellular space / extracellular region
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
2-PYRIDINETHIOL / Cathepsin B
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.1 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
DepositionMay 3, 1995Processing site: BNL
Revision 1.0Jul 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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
Remark 700SHEET THERE IS A BIFURCATED SHEET IN EACH MOLECULE. EACH IS REPRESENTED BY TWO SHEETS WITH SOME ...SHEET THERE IS A BIFURCATED SHEET IN EACH MOLECULE. EACH IS REPRESENTED BY TWO SHEETS WITH SOME STRANDS IN COMMON. THUS STRANDS 4, 5, 6 OF SHEETS SA1 AND SA2 ARE IDENTICAL TO STRANDS 2, 3, 4 OF SHEETS SA2 AND SB2 IN CHAINS A AND B, RESPECTIVELY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CATHEPSIN B
B: CATHEPSIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6944
Polymers55,4722
Non-polymers2222
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.070, 90.190, 62.210
Angle α, β, γ (deg.)90.00, 97.43, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: PRO A 117 - PRO A 118 OMEGA = 132.67 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.6461, 0.7292, 0.2254), (0.7297, -0.6767, 0.0974), (0.2235, 0.1015, -0.9694)
Vector: -52.144, 89, 94.152)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 1 .. 253 B 1 .. 253 0.347

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Components

#1: Protein CATHEPSIN B / Cathepsin


Mass: 27735.850 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: CDNA / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00787, cathepsin B
#2: Chemical ChemComp-PYS / 2-PYRIDINETHIOL / 2-Mercaptopyridine


Mass: 111.165 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5NS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCOMPND MOLECULE: CATHEPSIN B. RECOMBINANT RAT ENZYME. RESIDUE ASN 113 (BOTH CHAINS) IS NOT ...COMPND MOLECULE: CATHEPSIN B. RECOMBINANT RAT ENZYME. RESIDUE ASN 113 (BOTH CHAINS) IS NOT GLYCOSYLATED IN THIS STRUCTURE BECAUSE THE GLYCOSYLATION CONSENSUS SEQUENCE HAS BEEN MUTATED (SER115ALA) TO AVOID HETEROGENEOUS GLYCOSYLATION. CYSTEINE 29 AND PYRIDYL (HET) GROUP FORM DISULFIDE BOND IN BOTH MOLECULES A AND B.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.87 %
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

DetectorDate: Sep 1, 1989
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 28689 / % possible obs: 92.6 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.075
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å

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Processing

Software
NameClassification
SDMSdata collection
X-PLORmodel building
X-PLORrefinement
SDMSdata reduction
X-PLORphasing
RefinementResolution: 2.1→8 Å / σ(F): 2
Details: RESIDUE ASN 222 OF BOTH CHAINS HAS PHI-PSI ANGLES OUTSIDE THE NORMALLY PERMITTED RANGE BECAUSE ITS SIDE CHAIN OXYGEN ATOM IS INVOLVED IN A HYDROGEN BOND WITH THE ADJACENT MAIN-CHAIN N-H 223.
RfactorNum. reflection% reflection
Rwork0.166 --
obs0.166 24997 89.9 %
Displacement parametersBiso mean: 25.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3854 0 14 198 4066
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.46

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