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- PDB-4mpx: Human beta-tryptase co-crystal structure with [(1,1,3,3-tetrameth... -

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Basic information

Entry
Database: PDB / ID: 4mpx
TitleHuman beta-tryptase co-crystal structure with [(1,1,3,3-tetramethyldisiloxane-1,3-diyl)di-1-benzothiene-4,2-diyl]bis({4-[3-(aminomethyl)phenyl]piperidin-1-yl}methanone)
ComponentsTryptase alpha/beta-1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / coferon / alpha-hydroxyketone / small molecule inhibitor / drug discovery / self-assembly / crystal catalysis / silanol / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


tryptase / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / serine-type peptidase activity / defense response / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / 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 / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / 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 / 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-2AV / TRIETHYLENE GLYCOL / Tryptase alpha/beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWhite, A. / Stein, A.J. / Suto, R.
CitationJournal: To be Published
Title: Target-directed self-assembly of homodimeric drugs
Authors: Giardina, S.F. / Pingle, M. / Foreman, K.W. / Werner, D.S. / Bergstrom, D.E. / Barany, F. / Arnold, L.D.
History
DepositionSep 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptase alpha/beta-1
B: Tryptase alpha/beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,86113
Polymers54,9832
Non-polymers1,87811
Water5,567309
1
A: Tryptase alpha/beta-1
B: Tryptase alpha/beta-1
hetero molecules

A: Tryptase alpha/beta-1
B: Tryptase alpha/beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,72226
Polymers109,9664
Non-polymers3,75622
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area11530 Å2
ΔGint-196 kcal/mol
Surface area38300 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-89 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.310, 78.310, 165.722
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Tryptase alpha/beta-1 / Tryptase-1 / Tryptase I / Tryptase alpha-1


Mass: 27491.426 Da / Num. of mol.: 2 / Fragment: UNP residues 31-275
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPS1, TPS2, TPSAB1, TPSB1 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q15661, tryptase

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Non-polymers , 6 types, 320 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-2AV / [(1,1,3,3-tetramethyldisiloxane-1,3-diyl)di-1-benzothiene-4,2-diyl]bis({4-[3-(aminomethyl)phenyl]piperidin-1-yl}methanone)


Mass: 831.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H54N4O3S2Si2
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsN132K IS A NATURAL VARIANT.

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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: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.9 mg/mL protein incubated with compound 6A 30 minutes on ice prior to setup with 30% PEG1500, 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2011 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 40628 / Num. obs: 40587 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.093 / Χ2: 1.29 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.074.20.64140001.1781100
2.07-2.154.20.48440051.2181100
2.15-2.254.20.38739901.1771100
2.25-2.374.20.26640251.1771100
2.37-2.524.20.20840241.1551100
2.52-2.714.20.15440361.2071100
2.71-2.994.20.10840151.266199.9
2.99-3.424.20.07940831.606199.9
3.42-4.314.10.05541091.589199.6
4.31-5040.04543001.327199.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.78 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.832 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.168 / ESU R Free: 0.158 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2325 2015 5 %RANDOM
Rwork0.1845 ---
all0.1868 40576 --
obs0.1868 40361 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.18 Å2 / Biso mean: 31.6509 Å2 / Biso min: 16.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3820 0 116 309 4245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194090
X-RAY DIFFRACTIONr_bond_other_d0.0010.023766
X-RAY DIFFRACTIONr_angle_refined_deg2.061.9695600
X-RAY DIFFRACTIONr_angle_other_deg0.91538673
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.875489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.24923.315178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.74915588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2951525
X-RAY DIFFRACTIONr_chiral_restr0.1840.2591
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214565
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02954
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 153 -
Rwork0.26 2790 -
all-2943 -
obs--99.66 %

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