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- PDB-7h6h: THE 1.94 A CRYSTAL STRUCTURE OF HUMAN CATHEPSIN G IN COMPLEX WITH... -

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Basic information

Entry
Database: PDB / ID: 7h6h
TitleTHE 1.94 A CRYSTAL STRUCTURE OF HUMAN CATHEPSIN G IN COMPLEX WITH 1-[(7-fluoronaphthalen-1-yl)methyl]-3-[[methoxycarbonyl(methyl)amino]methyl]indole-2-carboxylic acid
ComponentsCathepsin G
KeywordsHYDROLASE / HUMAN CATHEPSIN G / SERINE PROTEINASE / COMPLEX (SERINE PROTEASE-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 / Purinergic signaling in leishmaniasis infection / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / Degradation of the extracellular matrix / serine-type peptidase activity / protein maturation / secretory granule / cytokine-mediated signaling pathway / protein processing / positive regulation of immune response / platelet activation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cytoplasmic stress granule / azurophil granule lumen / antibacterial humoral response / peptidase activity / heparin binding / cellular response to lipopolysaccharide / : / defense response to Gram-negative bacterium / lysosome / defense response to Gram-positive bacterium / immune response / protein phosphorylation / receptor ligand activity / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsBanner, D.W. / Benz, J.M. / Schlatter, D. / Hilpert, H.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Not funded Switzerland
CitationJournal: To be published
Title: Crystal structures of human Chymase and Cathepsin G
Authors: Markus, R. / Tosstorff, A.
History
DepositionApr 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

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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)27,4805
Polymers26,8021
Non-polymers6784
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.210, 44.730, 67.270
Angle α, β, γ (deg.)90.00, 107.08, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-303-

SO4

21A-578-

HOH

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Components

#1: Protein Cathepsin G / CG


Mass: 26801.787 Da / Num. of mol.: 1 / Mutation: NO
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSG / Production host: Escherichia coli (E. coli) / References: UniProt: P08311, cathepsin G
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1AO6 / 1-[(7-fluoronaphthalen-1-yl)methyl]-3-{[(methoxycarbonyl)(methyl)amino]methyl}-1H-indole-2-carboxylic acid


Mass: 420.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H21FN2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: 0.2 M LiSO4 (Salt), 25 %w/v PEG3350 (Precipitant), 0.1 M HEPES 7.5 pH (Buffer), Protein was at 17 mg/mL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.94→19.51 Å / Num. obs: 15390 / % possible obs: 89.9 % / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.091 / Net I/σ(I): 14.83 / Num. measured all: 65573
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Rmerge(I) obsNum. measured obsNum. unique obsRrim(I) allNet I/σ(I) obs
1.94-2.0689.90.3981060125050.4553.6
2.06-2.292.20.2841017323510.3245.72
2.2-2.37660.196649815410.2247.53
2.37-2.5993.90.124885020510.14211.68
2.59-2.8994.60.09820619040.10315.31
2.89-3.3395.50.057726816980.06521.85
3.33-4.0496.40.043614214470.04927.71
4.04-5.697.10.033494211800.03834.99
5.6-19.5194.40.03728937130.04331.77

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→19.51 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.91 / SU B: 7.898 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23162 779 5.1 %RANDOM
Rwork0.1706 ---
obs0.17363 14611 90.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-0 Å20.44 Å2
2--0.49 Å2-0 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.94→19.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 42 233 2061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0121887
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161808
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.832554
X-RAY DIFFRACTIONr_angle_other_deg0.4251.8064101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7015227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.256535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66210320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022397
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02533
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4961.033905
X-RAY DIFFRACTIONr_mcbond_other0.4941.033905
X-RAY DIFFRACTIONr_mcangle_it0.8671.8571133
X-RAY DIFFRACTIONr_mcangle_other0.8671.8591134
X-RAY DIFFRACTIONr_scbond_it0.731.174982
X-RAY DIFFRACTIONr_scbond_other0.7211.16975
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1972.0881410
X-RAY DIFFRACTIONr_long_range_B_refined5.6812.392102
X-RAY DIFFRACTIONr_long_range_B_other5.23310.692034
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 58 -
Rwork0.254 1045 -
obs--88.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5568-0.0875-0.70350.5913-0.25721.5810.10040.10770.11620.0536-0.00870.0012-0.1004-0.1453-0.09160.08420.045-0.01210.12560.01570.033714.91935.926621.9662
22.039-0.2699-0.63320.45610.13341.3001-0.02740.033-0.13720.07460.00430.07020.1233-0.120.02310.08780.0197-0.01360.12430.01360.040814.6948-4.084623.9026
32.0889-0.3391-0.74311.49370.92542.10380.07230.3230.0910.0929-0.02250.00130.0095-0.1192-0.04970.08560.032-0.00280.16270.02720.007322.34433.643410.7108
42.242-0.9942-1.17151.72520.20831.57390.11890.18560.0538-0.1542-0.0245-0.1712-0.06370.0596-0.09430.0780.0247-0.00650.1753-0.0040.045331.58310.29339.0025
51.38670.0067-0.80710.8401-0.21551.81970.00170.2042-0.1104-0.0408-0.019-0.01220.1876-0.11530.01740.08720.0252-0.02880.1458-0.00830.022322.2698-5.502114.2102
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 80
2X-RAY DIFFRACTION2A81 - 123
3X-RAY DIFFRACTION3A124 - 155
4X-RAY DIFFRACTION4A156 - 196
5X-RAY DIFFRACTION5A197 - 244

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