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- PDB-4o97: Crystal structure of matriptase in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 4o97
TitleCrystal structure of matriptase in complex with inhibitor
Components
  • Peptide CGLR
  • Suppressor of tumorigenicity 14 protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / MATRIPTASE / Trypsin-like serine proteinase fold / Protease / Small molecule inhibitor / 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
Chem-NTX / Suppressor of tumorigenicity 14 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRao, K.N. / Chandra, B.R. / Ashok, K.N. / Chakshusmathi, G. / Ramesh, K.S. / Subramanya, H.S.
CitationJournal: Bioorg.Med.Chem. / Year: 2014
Title: Structure-guided discovery of 1,3,5 tri-substituted benzenes as potent and selective matriptase inhibitors exhibiting in vivo antitumor efficacy.
Authors: Goswami, R. / Mukherjee, S. / Ghadiyaram, C. / Wohlfahrt, G. / Sistla, R.K. / Nagaraj, J. / Satyam, L.K. / Subbarao, K. / Palakurthy, R.K. / Gopinath, S. / Krishnamurthy, N.R. / Ikonen, T. / ...Authors: Goswami, R. / Mukherjee, S. / Ghadiyaram, C. / Wohlfahrt, G. / Sistla, R.K. / Nagaraj, J. / Satyam, L.K. / Subbarao, K. / Palakurthy, R.K. / Gopinath, S. / Krishnamurthy, N.R. / Ikonen, T. / Moilanen, A. / Subramanya, H.S. / Kallio, P. / Ramachandra, M.
History
DepositionJan 2, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 28, 2014Provider: 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 1.2Oct 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
B: Peptide CGLR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4273
Polymers26,9122
Non-polymers5151
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-4 kcal/mol
Surface area10380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.980, 140.503, 51.540
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-1064-

HOH

21A-1090-

HOH

31A-1138-

HOH

41A-1154-

HOH

51A-1168-

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 Peptide CGLR


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
#3: Chemical ChemComp-NTX / N-(trans-4-aminocyclohexyl)-3,5-bis[(3-carbamimidoylbenzyl)oxy]benzamide


Mass: 514.619 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H34N6O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.1M Tris pH 8.3, 0.2M MgCl2, 20% PEG 8000 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5416 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: 1.5416 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 18653 / % possible obs: 95.2 % / Redundancy: 2.8 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 13.1
Reflection shellResolution: 1.9→1.98 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1985 / % possible all: 89.7

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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: 2.2→25.91 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.867 / SU B: 6.891 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.361 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2766 627 5.2 %RANDOM
Rwork0.1863 ---
obs0.19081 11435 94.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.907 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2---0.05 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1885 0 38 207 2130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021953
X-RAY DIFFRACTIONr_angle_refined_deg1.8741.9592630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1435227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49123.61483
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1515290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.091512
X-RAY DIFFRACTIONr_chiral_restr0.1170.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211465
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 41 -
Rwork0.192 799 -
obs--98.13 %

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