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- PDB-1cgh: Human cathepsin G -

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Basic information

Entry
Database: PDB / ID: 1cgh
TitleHuman cathepsin G
ComponentsCATHEPSIN G
KeywordsHYDROLASE/HYDROLASE INHIBITOR / INFLAMMATION / SPECIFICITY / SERINE PROTEASE / 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 / 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
PHOSPHONATE INHIBITOR SUC-VAL-PRO-PHEP-(OPH)2 / Chem-1ZG / Cathepsin G
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHof, P. / Bode, W.
CitationJournal: EMBO J. / Year: 1996
Title: The 1.8 A crystal structure of human cathepsin G in complex with Suc-Val-Pro-PheP-(OPh)2: a Janus-faced proteinase with two opposite specificities.
Authors: Hof, P. / Mayr, I. / Huber, R. / Korzus, E. / Potempa, J. / Travis, J. / Powers, J.C. / Bode, W.
History
DepositionJun 26, 1996Processing site: BNL
Revision 1.0Jul 7, 1997Provider: 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 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)25,9822
Polymers25,4841
Non-polymers4971
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.040, 63.610, 79.720
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-1ZG / N-(3-carboxypropanoyl)-L-valyl-N-{(1R)-1-[(S)-hydroxy(oxido)phosphanyl]-2-phenylethyl}-L-prolinamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 497.479 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H32N3O8P / References: PHOSPHONATE INHIBITOR SUC-VAL-PRO-PHEP-(OPH)2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
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: 1.95 Å3/Da / Density % sol: 37 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Conc.: 1.2 M / Common name: citrate

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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: 95.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.057
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. measured all: 68129
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.86 Å / % possible obs: 95.3 % / Rmerge(I) obs: 0.327

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
Agrovatadata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BOVINE BETA TRYPSIN (W.BODE)

Resolution: 1.8→6 Å / σ(F): 0
Details: RESIDUES SER A 36A AND PRO A 36B ARE NOT DEFINED IN ELECTRON DENSITY AND THUS NOT WEIGHTED IN THE REFINEMENT. RESIDUES SER A 36A AND PRO A 36B ARE NOT DEFINED IN ELECTRON DENSITY AND THUS ...Details: RESIDUES SER A 36A AND PRO A 36B ARE NOT DEFINED IN ELECTRON DENSITY AND THUS NOT WEIGHTED IN THE REFINEMENT. RESIDUES SER A 36A AND PRO A 36B ARE NOT DEFINED IN ELECTRON DENSITY AND THUS NOT WEIGHTED IN THE REFINEMENT.
RfactorNum. reflection% reflection
Rfree0.24 -10 %
Rwork0.19 --
obs0.19 18433 94.2 %
Displacement parametersBiso mean: 22.43 Å2
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 33 145 1964
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.765
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_it2.05
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 17840
Solvent computation
*PLUS
Displacement parameters
*PLUS

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