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- PDB-5tp0: Human mesotrypsin in complex with diminazene -

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Basic information

Entry
Database: PDB / ID: 5tp0
TitleHuman mesotrypsin in complex with diminazene
ComponentsTrypsin-3
KeywordsHydrolase/Hydrolase Inhibitor / trypsin / serine-type endopeptidase / serine hydrolase / complex with small molecule drug / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


Uptake of dietary cobalamins into enterocytes / antimicrobial humoral response / Alpha-defensins / zymogen activation / Antimicrobial peptides / endothelial cell migration / trypsin / digestion / serine-type peptidase activity / tertiary granule lumen ...Uptake of dietary cobalamins into enterocytes / antimicrobial humoral response / Alpha-defensins / zymogen activation / Antimicrobial peptides / endothelial cell migration / trypsin / digestion / serine-type peptidase activity / tertiary granule lumen / serine-type endopeptidase activity / calcium ion binding / Neutrophil degranulation / proteolysis / extracellular space / extracellular region
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine 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 ...Serine proteases, trypsin family, histidine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsKayode, O. / Soares, A. / Radisky, E.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA154387 United States
CitationJournal: PLoS ONE / Year: 2017
Title: Small molecule inhibitors of mesotrypsin from a structure-based docking screen.
Authors: Kayode, O. / Huang, Z. / Soares, A.S. / Caulfield, T.R. / Dong, Z. / Bode, A.M. / Radisky, E.S.
History
DepositionOct 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trypsin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9797
Polymers24,2731
Non-polymers7066
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-58 kcal/mol
Surface area9700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.916, 64.443, 80.675
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Trypsin-3 / Brain trypsinogen / Mesotrypsinogen / Serine protease 3 / Serine protease 4 / Trypsin III / Trypsin IV


Mass: 24273.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: pancreas / Gene: PRSS3, PRSS4, TRY3, TRY4 / Organ: pancreas / Plasmid: pTRAP-T7-wtHu3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35030, trypsin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BRN / BERENIL / DIMINAZINE ACETURATE / 1,3-TRIS-(4'AMIDINOPHENYL)TRIAZINE


Mass: 281.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15N7 / Comment: medication*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES 2 M Ammonium Sulfate 2 % PEG-400 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 58825 / % possible obs: 98.4 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.045 / Net I/av σ(I): 52.057 / Net I/σ(I): 11.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.25-1.274.50.2220.954182.3
1.27-1.295.30.2150.962191.4
1.29-1.326.40.1920.977195.2
1.32-1.358.20.1750.988199.7
1.35-1.3810.10.1680.99199.7
1.38-1.4111.40.1510.9931100
1.41-1.4412.50.1320.995199.9
1.44-1.4812.10.1180.996199.9
1.48-1.5312.40.1060.9961100
1.53-1.5712.10.0940.9971100
1.57-1.6312.80.0840.9981100
1.63-1.712.30.0730.9981100
1.7-1.7712.40.0650.9981100
1.77-1.8712.30.060.9981100
1.87-1.98130.0510.9991100
1.98-2.1412.30.0470.9991100
2.14-2.3512.60.0440.9991100
2.35-2.6912.90.040.9991100
2.69-3.3912.30.0350.9991100
3.39-5011.90.0281199.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H4W

1h4w


Resolution: 1.25→32.24 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.915 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.033
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1372 2960 5 %RANDOM
Rwork0.1178 ---
obs0.1188 55799 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 128.08 Å2 / Biso mean: 11.612 Å2 / Biso min: 3.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å2-0 Å2-0 Å2
2--0.65 Å2-0 Å2
3----1.4 Å2
Refinement stepCycle: final / Resolution: 1.25→32.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1702 0 32 226 1960
Biso mean--21.31 27.45 -
Num. residues----224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0191855
X-RAY DIFFRACTIONr_bond_other_d0.0010.021699
X-RAY DIFFRACTIONr_angle_refined_deg2.1741.9592546
X-RAY DIFFRACTIONr_angle_other_deg1.0253.0043926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6225247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42224.60576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.14615294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.96158
X-RAY DIFFRACTIONr_chiral_restr0.1530.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212163
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02429
X-RAY DIFFRACTIONr_rigid_bond_restr6.77433554
X-RAY DIFFRACTIONr_sphericity_free50.57561
X-RAY DIFFRACTIONr_sphericity_bonded13.88553666
LS refinement shellResolution: 1.25→1.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 175 -
Rwork0.192 3437 -
all-3612 -
obs--82.88 %

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