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- PDB-1gmy: Cathepsin B complexed with dipeptidyl nitrile inhibitor -

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Basic information

Entry
Database: PDB / ID: 1gmy
TitleCathepsin B complexed with dipeptidyl nitrile inhibitor
ComponentsCATHEPSIN BCathepsin
KeywordsHYDROLASE/INHIBITOR / COMPLEX (HYDROLASE-INHIBITOR) / COVALENT COMPLEX / PROTEASE / CATHEPSIN B / HYDROLASE / THIOL PROTEASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


cathepsin B / peptidase inhibitor complex / thyroid hormone generation / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / decidualization ...cathepsin B / peptidase inhibitor complex / thyroid hormone generation / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / decidualization / collagen catabolic process / cysteine-type peptidase activity / epithelial cell differentiation / collagen binding / MHC class II antigen presentation / proteolysis involved in protein catabolic process / melanosome / peptidase activity / regulation of apoptotic process / collagen-containing extracellular matrix / ficolin-1-rich granule lumen / lysosome / symbiont entry into host cell / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / Neutrophil degranulation / perinuclear region of cytoplasm / proteolysis / extracellular space / extracellular exosome / 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-AMINOETHANIMIDIC ACID / 3-METHYLPHENYLALANINE / DIPHENYLACETIC ACID / Cathepsin B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGreenspan, P.D. / Clark, K.L. / Tommasi, R.A. / Cowen, S.D. / McQuire, L.W. / Farley, D.L. / van Duzer, J.H. / Goldberg, R.L. / Zhou, H. / Du, Z. ...Greenspan, P.D. / Clark, K.L. / Tommasi, R.A. / Cowen, S.D. / McQuire, L.W. / Farley, D.L. / van Duzer, J.H. / Goldberg, R.L. / Zhou, H. / Du, Z. / Fitt, J.J. / Coppa, D.E. / Fang, Z. / Macchia, W. / Zhu, L. / Capparelli, M.P. / Goldstein, R. / Wigg, A.M. / Doughty, J.R. / Bohacek, R.S. / Knap, A.K.
CitationJournal: J.Med.Chem. / Year: 2001
Title: Identification of Dipeptidyl Nitriles as Potent and Selective Inhibitors of Cathepsin B Through Structure-Based Drug Design
Authors: Greenspan, P.D. / Clark, K.L. / Tommasi, R.A. / Cowen, S.D. / Mcquire, L.W. / Farley, D.L. / Van Duzer, J.H. / Goldberg, R.L. / Zhou, H. / Du, Z. / Fitt, J.J. / Coppa, D.E. / Fang, Z. / ...Authors: Greenspan, P.D. / Clark, K.L. / Tommasi, R.A. / Cowen, S.D. / Mcquire, L.W. / Farley, D.L. / Van Duzer, J.H. / Goldberg, R.L. / Zhou, H. / Du, Z. / Fitt, J.J. / Coppa, D.E. / Fang, Z. / Macchia, W. / Zhu, L. / Capparelli, M.P. / Goldstein, R. / Wigg, A.M. / Doughty, J.R. / S Bohacek, R. / Knap, A.K.
History
DepositionSep 25, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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
C: CATHEPSIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,81212
Polymers86,4633
Non-polymers1,3499
Water11,349630
1
A: CATHEPSIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2714
Polymers28,8211
Non-polymers4503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CATHEPSIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2714
Polymers28,8211
Non-polymers4503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: CATHEPSIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2714
Polymers28,8211
Non-polymers4503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)103.900, 103.900, 125.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11C-2172-

HOH

21C-2203-

HOH

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Components

#1: Protein CATHEPSIN B / Cathepsin


Mass: 28821.123 Da / Num. of mol.: 3 / Fragment: PROTEASE DOMAIN, RESIDUES 80-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P07858, cathepsin B
#2: Chemical ChemComp-AEM / 2-AMINOETHANIMIDIC ACID


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6N2
#3: Chemical ChemComp-APD / 3-METHYLPHENYLALANINE


Mass: 179.216 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H13NO2
#4: Chemical ChemComp-DFA / DIPHENYLACETIC ACID


Mass: 212.244 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H12O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 630 / 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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growpH: 5.5 / Details: pH 5.50
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
250 mlsodium acetate1reservoirpH5.5
3100 mM1reservoirKCl
415-20 %PEG5000 MME1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Apr 15, 1995 / Details: YALE MIRROR
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→18 Å / Num. obs: 62966 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 12.2
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 3.7 / % possible all: 99.8
Reflection
*PLUS
Num. obs: 62967
Reflection shell
*PLUS
Num. unique obs: 10318

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Processing

Software
NameVersionClassification
CNX2000refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→18 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: BULK SOLVENT MODELING / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.199 5971 10.1 %RANDOM
Rwork0.161 ---
obs-59016 95 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.6375 Å2 / ksol: 0.391076 e/Å3
Displacement parametersBiso mean: 22.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 1.9→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5830 0 93 630 6553
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it1.972
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.207 909 10.1 %
Rwork0.167 8097 -
obs--88.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMNII.TOPOLOGY
X-RAY DIFFRACTION3NII.PARAMETER
Refinement
*PLUS
Highest resolution: 1.9 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.198 / Rfactor Rwork: 0.159
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88
LS refinement shell
*PLUS
Rfactor Rfree: 0.206 / Rfactor Rwork: 0.165

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