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- PDB-4r0i: CRYSTAL STRUCTURE of MATRIPTASE in COMPLEX WITH INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 4r0i
TitleCRYSTAL STRUCTURE of MATRIPTASE in COMPLEX WITH INHIBITOR
Components
  • SERINE PROTEASE, MATRIPTASE, MEMBRANE-TYPE SERINE PROTEASE 1, MT-SP1
  • Suppressor of tumorigenicity 14 protein
KeywordsHYDROLASE / MATRIPTASE / COMPLEX STRUCTURE / Trypsin-like serine proteinase fold / Protease / Small molecule inhibitor
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 / protein catabolic process / neural tube closure / basolateral plasma membrane / serine-type endopeptidase activity / external side of plasma membrane ...matriptase / epithelial cell morphogenesis involved in placental branching / Formation of the cornified envelope / keratinocyte differentiation / serine-type peptidase activity / protein catabolic process / neural tube closure / basolateral plasma membrane / serine-type endopeptidase activity / external side of plasma membrane / 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 / Spermadhesin, CUB domain superfamily / CUB domain profile. ...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 / Spermadhesin, CUB domain superfamily / CUB domain profile. / 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
Chem-3KM / Suppressor of tumorigenicity 14 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRao, K.N. / Ashok, K.N. / Chakshusmathi, G. / Rajeev, G. / Subramanya, H.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2015
Title: Discovery of O-(3-carbamimidoylphenyl)-l-serine amides as matriptase inhibitors using a fragment-linking approach
Authors: Goswami, R. / Wohlfahrt, G. / Mukherjee, S. / Ghadiyaram, C. / Nagaraj, J. / Satyam, L.K. / Subbarao, K. / Gopinath, S. / Krishnamurthy, N.R. / Subramanya, H.S. / Ramachandra, M.
History
DepositionJul 31, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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 / 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Suppressor of tumorigenicity 14 protein
B: SERINE PROTEASE, MATRIPTASE, MEMBRANE-TYPE SERINE PROTEASE 1, MT-SP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4363
Polymers26,9122
Non-polymers5241
Water1,49583
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-4 kcal/mol
Surface area10460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.842, 140.448, 51.899
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-1018-

HOH

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Components

#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 / Fragment: UNP residues 615-855
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ST14, PRSS14, SNC19, TADG15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y5Y6, matriptase
#2: Protein/peptide SERINE PROTEASE, MATRIPTASE, MEMBRANE-TYPE SERINE PROTEASE 1, MT-SP1 / 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: 448.561 Da / Num. of mol.: 1 / Fragment: UNP residues 604-607
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ST14, PRSS14, SNC19, TADG15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y5Y6, matriptase
#3: Chemical ChemComp-3KM / 3-({(2S)-3-[4-(2-aminoethyl)piperidin-1-yl]-2-[(naphthalen-2-ylsulfonyl)amino]-3-oxopropyl}oxy)benzenecarboximidamide


Mass: 523.647 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N5O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: vapor diffusion, hanging drop / pH: 8.3
Details: 0.1M Tris pH 8.3 0.2M MgCl2, 20% PEG8000 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Details: Mirrors
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 18801 / % possible obs: 95.5 % / Redundancy: 2.5 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 10.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1898 / Rsym value: 0.239 / % possible all: 98.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EAX

1eax


Resolution: 1.9→28.1 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.871 / SU B: 4.705 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28857 960 5.1 %RANDOM
Rwork0.21976 ---
obs0.22325 17840 95.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.697 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1886 0 37 83 2006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191952
X-RAY DIFFRACTIONr_bond_other_d00.0212
X-RAY DIFFRACTIONr_angle_refined_deg1.8641.9592630
X-RAY DIFFRACTIONr_angle_other_deg0.75326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3125227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27523.61483
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59215290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.11512
X-RAY DIFFRACTIONr_chiral_restr0.1210.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211459
X-RAY DIFFRACTIONr_gen_planes_other0.0010.028
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 75 -
Rwork0.221 1221 -
obs--98.33 %

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