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- PDB-8g1v: Crystal Structure Matriptase (C731S) in Complex with Inhibitor MM... -

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Basic information

Entry
Database: PDB / ID: 8g1v
TitleCrystal Structure Matriptase (C731S) in Complex with Inhibitor MM1132-2
ComponentsSuppressor of tumorigenicity 14 protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / MATRIPTASE / INHIBITOR COMPLEX / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


matriptase / epithelial cell morphogenesis involved in placental branching / acrosome reaction / 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 ...matriptase / epithelial cell morphogenesis involved in placental branching / acrosome reaction / 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 domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
: / Suppressor of tumorigenicity 14 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsLovell, S. / Kashipathy, M.M. / Battaile, K.P. / Janetka, J.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: Protein Sci. / Year: 2024
Title: Use of protease substrate specificity screening in the rational design of selective protease inhibitors with unnatural amino acids: Application to HGFA, matriptase and hepsin
Authors: Lovell, S. / Janetka, J.W.
History
DepositionFeb 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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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)27,80513
Polymers26,4481
Non-polymers1,35712
Water5,927329
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.473, 149.473, 58.501
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-1057-

HOH

21A-1257-

HOH

31A-1319-

HOH

41A-1329-

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: 26447.689 Da / Num. of mol.: 1 / Fragment: residues 615-855 / Mutation: C731S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ST14, PRSS14, SNC19, TADG15 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y5Y6, matriptase

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Non-polymers , 5 types, 341 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-YIL / N~2~-{[3-(acetamidomethyl)phenyl]acetyl}-N-[(2S)-1-(1,3-benzothiazol-2-yl)-5-carbamimidamido-1,1-dihydroxypentan-2-yl]-L-leucinamide


Mass: 611.755 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H41N7O5S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2M ammonium sulfate, 100 sodium cacodylate, 200 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 17, 2020
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→48.93 Å / Num. obs: 84315 / % possible obs: 100 % / Redundancy: 19.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.025 / Rrim(I) all: 0.112 / Χ2: 1.01 / Net I/σ(I): 15.8 / Num. measured all: 1679591
Reflection shellResolution: 1.35→1.37 Å / % possible obs: 100 % / Redundancy: 17.3 % / Rmerge(I) obs: 1.658 / Num. measured all: 71214 / Num. unique obs: 4119 / CC1/2: 0.792 / Rpim(I) all: 0.41 / Rrim(I) all: 1.709 / Χ2: 1.05 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX1.19rc3_4028refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ncl

3ncl


Resolution: 1.35→35.9 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 13.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.152 4293 5.09 %
Rwork0.1309 --
obs0.132 84276 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1841 0 79 329 2249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072005
X-RAY DIFFRACTIONf_angle_d0.9632742
X-RAY DIFFRACTIONf_dihedral_angle_d13.179707
X-RAY DIFFRACTIONf_chiral_restr0.087289
X-RAY DIFFRACTIONf_plane_restr0.009354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.24071250.22772654X-RAY DIFFRACTION100
1.37-1.380.25991190.21682630X-RAY DIFFRACTION100
1.38-1.40.21651360.19012653X-RAY DIFFRACTION100
1.4-1.420.24091410.16942607X-RAY DIFFRACTION100
1.42-1.430.22461640.1582615X-RAY DIFFRACTION100
1.43-1.450.17461540.152607X-RAY DIFFRACTION100
1.45-1.480.17551300.14612632X-RAY DIFFRACTION100
1.48-1.50.19021720.1442628X-RAY DIFFRACTION100
1.5-1.520.16821220.14422634X-RAY DIFFRACTION100
1.52-1.550.17081450.14282656X-RAY DIFFRACTION100
1.55-1.570.14211470.1292618X-RAY DIFFRACTION100
1.57-1.60.14421250.12142638X-RAY DIFFRACTION100
1.6-1.630.14991390.11172662X-RAY DIFFRACTION100
1.63-1.660.13511600.10592624X-RAY DIFFRACTION100
1.66-1.70.10661340.10062646X-RAY DIFFRACTION100
1.7-1.740.12191390.10432651X-RAY DIFFRACTION100
1.74-1.780.12461240.09852674X-RAY DIFFRACTION100
1.78-1.830.12141460.10842659X-RAY DIFFRACTION100
1.83-1.890.13611350.11652659X-RAY DIFFRACTION100
1.89-1.950.13221370.12352657X-RAY DIFFRACTION100
1.95-2.020.14041450.12052670X-RAY DIFFRACTION100
2.02-2.10.13021450.12012650X-RAY DIFFRACTION100
2.1-2.190.14211410.12162678X-RAY DIFFRACTION100
2.19-2.310.11841460.11812673X-RAY DIFFRACTION100
2.31-2.450.13221460.11632699X-RAY DIFFRACTION100
2.45-2.640.13961450.12642701X-RAY DIFFRACTION100
2.64-2.910.17591470.13912709X-RAY DIFFRACTION100
2.91-3.330.16951680.13512712X-RAY DIFFRACTION100
3.33-4.190.15431720.1282747X-RAY DIFFRACTION100
4.19-35.90.16631440.15392940X-RAY DIFFRACTION100

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