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- PDB-6n4t: Crystal structure of Matriptase1 in complex with a peptidomimetic... -

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Basic information

Entry
Database: PDB / ID: 6n4t
TitleCrystal structure of Matriptase1 in complex with a peptidomimetic benzothiazole
ComponentsSuppressor of tumorigenicity 14 protein
Keywordshydrolase/hydrolase inhibitor / inhibitor complex / HYDROLASE / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


matriptase / epithelial cell morphogenesis involved in placental branching / Formation of the cornified envelope / keratinocyte differentiation / serine-type peptidase activity / neural tube closure / protein catabolic process / basolateral plasma membrane / external side of plasma membrane / serine-type endopeptidase activity ...matriptase / epithelial cell morphogenesis involved in placental branching / Formation of the cornified envelope / keratinocyte differentiation / serine-type peptidase activity / neural tube closure / protein catabolic process / basolateral plasma membrane / external side of plasma membrane / serine-type endopeptidase activity / proteolysis / extracellular space / plasma membrane
Similarity search - Function
Peptidase S1A, matripase / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily ...Peptidase S1A, matripase / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / 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
N-(3-phenylpropanoyl)-3-(1,3-thiazol-4-yl)-L-alanyl-N-[(1S,2S)-1-(1,3-benzothiazol-2-yl)-5-carbamimidamido-1-hydroxypentan-2-yl]-L-valinamide / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / ETHANOL / GLUTATHIONE / Chem-KD7 / Suppressor of tumorigenicity 14 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.945 Å
AuthorsCampobasso, N.
CitationJournal: Cell Chem Biol / Year: 2019
Title: Discovery and Development of TMPRSS6 Inhibitors Modulating Hepcidin Levels in Human Hepatocytes.
Authors: Beliveau, F. / Tarkar, A. / Dion, S.P. / Desilets, A. / Ghinet, M.G. / Boudreault, P.L. / St-Georges, C. / Marsault, E. / Paone, D. / Collins, J. / Macphee, C.H. / Campobasso, N. / Groy, A. ...Authors: Beliveau, F. / Tarkar, A. / Dion, S.P. / Desilets, A. / Ghinet, M.G. / Boudreault, P.L. / St-Georges, C. / Marsault, E. / Paone, D. / Collins, J. / Macphee, C.H. / Campobasso, N. / Groy, A. / Cottom, J. / Ouellette, M. / Pope, A.J. / Leduc, R.
History
DepositionNov 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Suppressor of tumorigenicity 14 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6426
Polymers26,4641
Non-polymers1,1795
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.029, 141.519, 52.109
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-481-

HOH

21A-506-

HOH

31A-519-

HOH

41A-530-

HOH

51A-569-

HOH

61A-578-

HOH

71A-579-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Suppressor of tumorigenicity 14 protein / Matriptase / Membrane-type serine protease 1 / MT-SP1 / Prostamin / Serine protease 14 / Serine ...Matriptase / Membrane-type serine protease 1 / MT-SP1 / Prostamin / Serine protease 14 / Serine protease TADG-15 / Tumor-associated differentially-expressed gene 15 protein


Mass: 26463.756 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ST14, PRSS14, SNC19, TADG15 / Plasmid: pET28a-Mtsp (615-855) / Production host: Eschericia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y5Y6, matriptase

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Non-polymers , 6 types, 185 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#4: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#5: Chemical ChemComp-KD7 / N-(3-phenylpropanoyl)-3-(1,3-thiazol-4-yl)-L-alanyl-N-[(1S,2S)-1-(1,3-benzothiazol-2-yl)-5-carbamimidamido-1-hydroxypentan-2-yl]-L-valinamide


Type: Peptide-like / Class: Inhibitor / Mass: 678.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H42N8O4S2 / Feature type: SUBJECT OF INVESTIGATION
References: N-(3-phenylpropanoyl)-3-(1,3-thiazol-4-yl)-L-alanyl-N-[(1S,2S)-1-(1,3-benzothiazol-2-yl)-5-carbamimidamido-1-hydroxypentan-2-yl]-L-valinamide
#6: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.33 Å3/Da / Density % sol: 47.32 %
Crystal growMethod: vapor diffusion, hanging drop
Details: 0.1 M Tris, pH 8.2 - 8.7, 18 % - 22 % PEG800, 200 mM MgCl2
PH range: 8.2 - 8.7 / Temp details: room temp

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.945→100 Å / Num. obs: 18515 / % possible obs: 99.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 16.44 Å2 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.089 / Rrim(I) all: 0.193 / Χ2: 0.921 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-1.983.70.698670.6380.3870.7961.14897
1.98-2.023.70.618830.7080.3390.7021.15498.3
2.02-2.063.80.5468730.7090.3030.6281.17798.9
2.06-2.13.80.4899220.7590.2720.5631.13999.1
2.1-2.1540.4648890.7660.2540.5321.1299.8
2.15-2.240.4099050.8330.2240.4691.12299.5
2.2-2.2540.3878990.8270.2150.4451.12399.6
2.25-2.314.10.3239070.880.1770.371.03699.8
2.31-2.384.10.3069190.8590.1660.351.11399.8
2.38-2.464.10.2718990.9080.1450.3091.03999.6
2.46-2.544.20.2419120.9230.1310.2760.91599.9
2.54-2.654.20.2329070.9150.1230.2640.93699.7
2.65-2.774.10.219300.9410.1110.2390.90899.9
2.77-2.914.20.1879040.9480.1010.2140.80399.7
2.91-3.14.20.169160.9660.0840.1810.76599.8
3.1-3.334.20.1399320.9690.0720.1570.696100
3.33-3.674.30.1299210.9750.0660.1460.64999.9
3.67-4.24.20.1299380.970.0650.1440.59599.7
4.2-5.294.20.1319450.9740.0660.1480.58799.5
5.29-1004.10.1569950.9590.0810.1770.6598.1

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
DENZOdata reduction
PHASERphasing
RefinementResolution: 1.945→38.577 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.16
RfactorNum. reflection% reflection
Rfree0.2254 922 4.98 %
Rwork0.165 --
obs0.1678 18515 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.83 Å2 / Biso mean: 16.252 Å2 / Biso min: 5.68 Å2
Refinement stepCycle: final / Resolution: 1.945→38.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 91 180 2129
Biso mean--22.79 24.23 -
Num. residues----241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071993
X-RAY DIFFRACTIONf_angle_d1.062708
X-RAY DIFFRACTIONf_chiral_restr0.06279
X-RAY DIFFRACTIONf_plane_restr0.005354
X-RAY DIFFRACTIONf_dihedral_angle_d15.771135
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9447-2.04720.24981350.18212331246694
2.0472-2.17550.20641190.167125282647100
2.1755-2.34340.22261250.168724882613100
2.3434-2.57920.22411350.174425122647100
2.5792-2.95230.27461470.181525092656100
2.9523-3.71910.21011390.159625542693100
3.7191-38.58480.21121220.150926712793100

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