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- PDB-8g1w: Crystal Structure Matriptase (C731S) in Complex with Inhibitor VD4162B -

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Basic information

Entry
Database: PDB / ID: 8g1w
TitleCrystal Structure Matriptase (C731S) in Complex with Inhibitor VD4162B
Components
  • Cyclic peptide inhibitor (ACE)Y(DTR)(NLE)(KCM)
  • Cyclic peptide inhibitor (ACE)Y(DTR)(NLE)(THZ)
  • Suppressor 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsLovell, S. / Kashipathy, M.M. / Battaile, K.P. / Janetka, J.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110761 United States
CitationJournal: J.Med.Chem. / Year: 2024
Title: Mechanism-Based Macrocyclic Inhibitors of Serine Proteases.
Authors: Damalanka, V.C. / Banas, V. / De Bona, P. / Kashipathy, M.M. / Battaile, K. / Lovell, S. / Janetka, J.W.
History
DepositionFeb 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Suppressor of tumorigenicity 14 protein
M: Cyclic peptide inhibitor (ACE)Y(DTR)(NLE)(THZ)
L: Cyclic peptide inhibitor (ACE)Y(DTR)(NLE)(KCM)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0454
Polymers28,0103
Non-polymers351
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-22 kcal/mol
Surface area10070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.259, 80.248, 40.361
Angle α, β, γ (deg.)90.00, 95.45, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1074-

HOH

21A-1157-

HOH

31A-1212-

HOH

41A-1251-

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: 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
#2: Protein/peptide Cyclic peptide inhibitor (ACE)Y(DTR)(NLE)(THZ)


Mass: 779.951 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide Cyclic peptide inhibitor (ACE)Y(DTR)(NLE)(KCM)


Mass: 781.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
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

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 2M sodium formate, 100 sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2020
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.2→40.18 Å / Num. obs: 74030 / % possible obs: 99.6 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.032 / Rpim(I) all: 0.02 / Rrim(I) all: 0.038 / Χ2: 0.52 / Net I/σ(I): 10.3 / Num. measured all: 248305
Reflection shellResolution: 1.2→1.22 Å / % possible obs: 99.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.457 / Num. measured all: 12004 / Num. unique obs: 3781 / CC1/2: 0.895 / Rpim(I) all: 0.301 / Rrim(I) all: 0.549 / Χ2: 0.47 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX1.19_4084refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ncl

3ncl


Resolution: 1.2→31.37 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 20.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1658 3736 5.05 %
Rwork0.1484 --
obs0.1493 73999 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→31.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1847 0 115 258 2220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072046
X-RAY DIFFRACTIONf_angle_d1.1642791
X-RAY DIFFRACTIONf_dihedral_angle_d15.228707
X-RAY DIFFRACTIONf_chiral_restr0.088286
X-RAY DIFFRACTIONf_plane_restr0.009362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.220.28961390.2632583X-RAY DIFFRACTION99
1.22-1.230.23461460.24172555X-RAY DIFFRACTION99
1.23-1.250.28311310.22772606X-RAY DIFFRACTION99
1.25-1.270.23021490.21662541X-RAY DIFFRACTION99
1.27-1.280.21851340.20662611X-RAY DIFFRACTION99
1.28-1.30.24391340.20122600X-RAY DIFFRACTION99
1.3-1.330.22151220.19022586X-RAY DIFFRACTION99
1.33-1.350.21291380.18572619X-RAY DIFFRACTION100
1.35-1.370.24841360.18012604X-RAY DIFFRACTION100
1.37-1.40.21661640.17222559X-RAY DIFFRACTION100
1.4-1.430.21971270.16792592X-RAY DIFFRACTION100
1.43-1.460.24411340.1622618X-RAY DIFFRACTION100
1.46-1.490.19371430.15762621X-RAY DIFFRACTION100
1.49-1.530.19731450.15472581X-RAY DIFFRACTION100
1.53-1.570.18261520.14082600X-RAY DIFFRACTION100
1.57-1.620.1651420.13952585X-RAY DIFFRACTION100
1.62-1.670.16841560.13222598X-RAY DIFFRACTION99
1.67-1.730.17351240.13932591X-RAY DIFFRACTION100
1.73-1.80.17081210.13922634X-RAY DIFFRACTION100
1.8-1.880.14951430.1362608X-RAY DIFFRACTION100
1.88-1.980.16281390.13342589X-RAY DIFFRACTION100
1.98-2.110.13011250.132642X-RAY DIFFRACTION100
2.11-2.270.15851340.13322609X-RAY DIFFRACTION99
2.27-2.50.13911360.14042629X-RAY DIFFRACTION99
2.5-2.860.15191390.15482607X-RAY DIFFRACTION100
2.86-3.60.15371320.14422638X-RAY DIFFRACTION100
3.6-31.370.15281510.14062657X-RAY DIFFRACTION100

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