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- PDB-1kyn: Cathepsin-G -

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Basic information

Entry
Database: PDB / ID: 1kyn
TitleCathepsin-G
Componentscathepsin G
KeywordsHYDROLASE / serine protease
Function / homology
Function and homology information


cathepsin G / biofilm matrix disassembly / neutrophil-mediated killing of gram-positive bacterium / purinergic nucleotide receptor signaling pathway / caspase binding / negative regulation of T cell activation / neutrophil activation / Suppression of apoptosis / Interleukin-1 processing / positive regulation of platelet aggregation ...cathepsin G / biofilm matrix disassembly / neutrophil-mediated killing of gram-positive bacterium / purinergic nucleotide receptor signaling pathway / caspase binding / negative regulation of T cell activation / neutrophil activation / Suppression of apoptosis / Interleukin-1 processing / positive regulation of platelet aggregation / Antimicrobial peptides / Activation of Matrix Metalloproteinases / monocyte chemotaxis / extracellular matrix disassembly / defense response to fungus / angiotensin maturation / Purinergic signaling in leishmaniasis infection / Metabolism of Angiotensinogen to Angiotensins / Degradation of the extracellular matrix / serine-type peptidase activity / secretory granule / protein processing / platelet activation / cytokine-mediated signaling pathway / cytoplasmic stress granule / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of immune response / azurophil granule lumen / antibacterial humoral response / peptidase activity / heparin binding / cellular response to lipopolysaccharide / collagen-containing extracellular matrix / defense response to Gram-negative bacterium / lysosome / defense response to Gram-positive bacterium / receptor ligand activity / immune response / protein phosphorylation / intracellular membrane-bounded organelle / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-KTP / Cathepsin G
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsGreco, M.N. / Hawkins, M.J. / Powell, E.T. / Almond Jr., H.R. / Corcoran, T.W. / De Garavilla, L. / Kauffman, J.A. / Recacha, R. / Chattopadhyay, D. / Andrade-Gordon, P. / Maryanoff, B.E.
CitationJournal: J.Am.Chem.Soc. / Year: 2002
Title: Nonpeptide inhibitors of cathepsin G: optimization of a novel beta-ketophosphonic acid lead by structure-based drug design.
Authors: Greco, M.N. / Hawkins, M.J. / Powell, E.T. / Almond Jr., H.R. / Corcoran, T.W. / de Garavilla, L. / Kauffman, J.A. / Recacha, R. / Chattopadhyay, D. / Andrade-Gordon, P. / Maryanoff, B.E.
History
DepositionFeb 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2002Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 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 G
B: cathepsin G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3564
Polymers53,6042
Non-polymers7532
Water00
1
A: cathepsin G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1782
Polymers26,8021
Non-polymers3761
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cathepsin G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1782
Polymers26,8021
Non-polymers3761
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.440, 59.440, 130.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein cathepsin G / CG


Mass: 26801.787 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08311, cathepsin G
#2: Chemical ChemComp-KTP / (2-NAPHTHALEN-2-YL-1-NAPHTHALEN-1-YL-2-OXO-ETHYL)-PHOSPHONIC ACID / BIS-NAPTHYL BETA-KETOPHOSPHONIC ACID


Mass: 376.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H17O4P
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: 2.15 Å3/Da / Density % sol: 42.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: ammonium sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 6, 1998
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.99→25 Å / Num. obs: 7354 / % possible obs: 79.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 8.2
Reflection shellResolution: 2.99→3.1 Å / Rmerge(I) obs: 0.2 / % possible all: 75

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→14.86 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 1184420.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.328 453 11 %RANDOM
Rwork0.258 ---
all-4111 --
obs-4111 72.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 104.618 Å2 / ksol: 0.615939 e/Å3
Displacement parametersBiso mean: 26 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 3.5→14.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3553 0 54 0 3607
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d27.6
X-RAY DIFFRACTIONc_improper_angle_d0.73
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.357 67 10 %
Rwork0.253 603 -
obs-603 72.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PAR.TXTTOP.TXT

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