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- PDB-2za5: Crystal Structure of human tryptase with potent non-peptide inhibitor -

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Basic information

Entry
Database: PDB / ID: 2za5
TitleCrystal Structure of human tryptase with potent non-peptide inhibitor
ComponentsTryptase beta 2
KeywordsHYDROLASE / Tryptase / serine protease / tetramer
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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / 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 ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / 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-2FF / Tryptase beta-2 / Tryptase alpha/beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSpurlino, J.C. / Barnakov, S.A. / Lewandowski, F. / Milligan, C.
Citation
Journal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Potent, nonpeptide inhibitors of human mast cell tryptase. Synthesis and biological evaluation of novel spirocyclic piperidine amide derivatives
Authors: Costanzo, M.J. / Yabut, S.C. / Zhang, H.-C. / White, K.B. / de Garavilla, L. / Wang, Y. / Minor, L.K. / Tounge, B.A. / Barnakov, A.N. / Lewandowski, F. / Milligan, C. / Spurlino, J.C. / ...Authors: Costanzo, M.J. / Yabut, S.C. / Zhang, H.-C. / White, K.B. / de Garavilla, L. / Wang, Y. / Minor, L.K. / Tounge, B.A. / Barnakov, A.N. / Lewandowski, F. / Milligan, C. / Spurlino, J.C. / Abraham, W.M. / Boswell-Smith, V. / Page, C.P. / Maryanoff, B.E.
#1: Journal: J.Med.Chem. / Year: 2003
Title: Potent, small-molecule inhibitors of human mast cell tryptase. Antiasthmatic action of a dipeptide-based transition-state analogue containing a benzothiazole ketone
Authors: Costanzo, M.J. / Yabut, S.C. / Almond, H.R. / Andrade-Gordon, P. / Corcoran, T.W. / de Garavilla, L. / Kauffman, J.A. / Abraham, W.M. / Recacha, R. / Chattopadhyay, D. / Maryanoff, B.E.
History
DepositionOct 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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 1.4Oct 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: Tryptase beta 2
B: Tryptase beta 2
C: Tryptase beta 2
D: Tryptase beta 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,6168
Polymers109,9664
Non-polymers1,6504
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9680 Å2
ΔGint-30.8 kcal/mol
Surface area38030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.678, 82.678, 170.284
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Tryptase beta 2


Mass: 27491.426 Da / Num. of mol.: 4 / Fragment: UNP residues 31-275
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) / References: UniProt: Q6B052, UniProt: P20231*PLUS, tryptase
#2: Chemical
ChemComp-2FF / (5-(aminomethyl)-2H-spiro[benzofuran-3,4'-piperidine]-1'-yl)(5-(phenylethynyl)furan-2-yl)methanone


Mass: 412.480 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H24N2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.1 / Details: pH 6.1, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 51904

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A0L

1a0l


Resolution: 2.3→19.915 Å / FOM work R set: 0.839 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2464 4.98 %RANDOM
Rwork0.181 ---
obs0.184 50943 97.88 %-
Solvent computationShrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.675 Å2 / ksol: 0.386 e/Å3
Displacement parametersBiso max: 83.59 Å2 / Biso mean: 21.16 Å2 / Biso min: 5.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.406 Å20 Å2-0 Å2
2--0.406 Å20 Å2
3----0.811 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7647 0 124 431 8202
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d1.2641
X-RAY DIFFRACTIONf_bond_d0.0091
X-RAY DIFFRACTIONf_chiral_restr0.0851
X-RAY DIFFRACTIONf_dihedral_angle_d24.2091
X-RAY DIFFRACTIONf_plane_restr0.0091
X-RAY DIFFRACTIONf_nbd_refined4.1321

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