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- PDB-4jzi: Crystal Structure of Matriptase in complex with Inhibitor". -

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Basic information

Entry
Database: PDB / ID: 4jzi
TitleCrystal Structure of Matriptase in complex with Inhibitor".
ComponentsSuppressor of tumorigenicity 14 protein
KeywordsHYDROLASE / MATRIPTASE / INHIBITOR / COMPLEX STRUCTURE
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
Chem-N4C / Suppressor of tumorigenicity 14 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSubramanya, H.S. / Chandra, R.B. / Ashok, K.N. / Chakshusmathi, G. / Ramesh, K.S.
CitationJournal: ACS MED.CHEM.LETT. / Year: 2013
Title: Discovery of Pyridyl Bis(oxy)dibenzimidamide Derivatives as Selective Matriptase Inhibitors
Authors: Goswami, R. / Mukherjee, S. / Wohlfahrt, G. / Ghadiyaram, C. / Nagaraj, J. / Chandra, B.R. / Sistla, R.K. / Satyam, L.K. / Samiulla, D.S. / Moilanen, A. / Subramanya, H.S. / Ramachandra, M.
History
DepositionApr 3, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Nov 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 1.3Oct 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9512
Polymers26,4641
Non-polymers4881
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.852, 140.841, 51.875
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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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: Chemical ChemComp-N4C / N-(trans-4-aminocyclohexyl)-2,6-bis(4-carbamimidoylphenoxy)pyridine-4-carboxamide


Mass: 487.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H29N7O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 291 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 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5416 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 7, 2007 / Details: Mirrors
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5416 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 30410 / Num. obs: 15482 / % possible obs: 91.2 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.108 / Mean I/σ(I) obs: 2.4 / % possible all: 94.2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
REFMAC5.2.0001refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EAX

1eax


Resolution: 2→28.06 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.905 / SU B: 3.926 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24362 784 5.1 %RANDOM
Rwork0.21735 ---
obs0.21871 14695 91.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.478 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2→28.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 36 30 1924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211973
X-RAY DIFFRACTIONr_bond_other_d0.0010.021731
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.9572683
X-RAY DIFFRACTIONr_angle_other_deg0.76734015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5235243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.47323.45284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33415293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0881513
X-RAY DIFFRACTIONr_chiral_restr0.0760.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022224
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02422
X-RAY DIFFRACTIONr_nbd_refined0.210.2402
X-RAY DIFFRACTIONr_nbd_other0.1940.21812
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.21021
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.255
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2920.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0960.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7031.51549
X-RAY DIFFRACTIONr_mcbond_other0.1271.5509
X-RAY DIFFRACTIONr_mcangle_it0.86121937
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.633923
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2564.5746
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: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.238 49
Rwork0.201 1098

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