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- PDB-1au8: HUMAN CATHEPSIN G -

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Basic information

Entry
Database: PDB / ID: 1au8
TitleHUMAN CATHEPSIN G
ComponentsCATHEPSIN G
KeywordsHYDROLASE/HYDROLASE INHIBITOR / INFLAMMATION / SPECIFICITY / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


cathepsin G / biofilm matrix disassembly / neutrophil-mediated killing of gram-positive bacterium / purinergic nucleotide receptor signaling pathway / negative regulation of T cell activation / caspase binding / Suppression of apoptosis / neutrophil activation / protein metabolic process / positive regulation of platelet aggregation ...cathepsin G / biofilm matrix disassembly / neutrophil-mediated killing of gram-positive bacterium / purinergic nucleotide receptor signaling pathway / negative regulation of T cell activation / caspase binding / Suppression of apoptosis / neutrophil activation / protein metabolic process / positive regulation of platelet aggregation / Interleukin-1 processing / Antimicrobial peptides / Activation of Matrix Metalloproteinases / monocyte chemotaxis / angiotensin maturation / extracellular matrix disassembly / defense response to fungus / Metabolism of Angiotensinogen to Angiotensins / Purinergic signaling in leishmaniasis infection / serine-type peptidase activity / Degradation of the extracellular matrix / 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 / heparin binding / peptidase activity / antibacterial humoral response / collagen-containing extracellular matrix / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / lysosome / receptor ligand activity / defense response to Gram-positive bacterium / immune response / protein phosphorylation / serine-type endopeptidase activity / intracellular membrane-bounded organelle / 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 domain profile. / Serine proteases, trypsin family, serine active site. / 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 domain profile. / Serine proteases, trypsin family, serine active site. / 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
N-(3-carboxypropanoyl)-L-valyl-N-[(1R)-5-amino-1-phosphonopentyl]-L-prolinamide / Chem-0H8 / Cathepsin G
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsMedrano, F.J. / Bode, W. / Banbula, A. / Potempa, J.
CitationJournal: to be published
Title: HUMAN CATHEPSIN G
Authors: Medrano, F.J. / Bode, W. / Banbula, A. / Potempa, J.
History
DepositionSep 12, 1997Processing site: BNL
Revision 1.0Oct 14, 1998Provider: 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
Remark 650 HELIX DETERMINATION METHOD: TAKEN FROM RELEASED PDB ENTRY 1CGH
Remark 700 SHEET DETERMINATION METHOD: TAKEN FROM RELEASED PDB ENTRY 1CGH

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CATHEPSIN G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9632
Polymers25,4841
Non-polymers4781
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.230, 63.460, 80.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CATHEPSIN G /


Mass: 25484.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08311, cathepsin G
#2: Chemical ChemComp-0H8 / N-(3-carboxypropanoyl)-L-valyl-N-[(1R)-5-amino-1-phosphonopentyl]-L-prolinamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 478.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H35N4O8P
References: N-(3-carboxypropanoyl)-L-valyl-N-[(1R)-5-amino-1-phosphonopentyl]-L-prolinamide
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 1.97 Å3/Da / Density % sol: 37.63 %
Crystal growpH: 7 / Details: pH 7.0

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 18433 / % possible obs: 96.3 % / Rmerge(I) obs: 0.134

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATA/AGROVATAdata reduction
X-PLOR3.851model building
X-PLOR3.851refinement
CCP4(AGROVATAdata scaling
ROTAVATA)data scaling
X-PLOR3.851phasing
RefinementResolution: 1.9→6 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.251 -10 %
Rwork0.186 --
obs0.186 15130 97.1 %
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 31 138 1955
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.874
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.87
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.44
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
LS refinement shellHighest resolution: 1.9 Å /
Num. reflection% reflection
Rwork15130 -
obs-97.1 %

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