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- PDB-5f03: TRYPTASE B2 IN COMPLEX WITH 5-(3-Aminomethyl-phenoxymethyl)-3-[3-... -

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Basic information

Entry
Database: PDB / ID: 5f03
TitleTRYPTASE B2 IN COMPLEX WITH 5-(3-Aminomethyl-phenoxymethyl)-3-[3-(2-chloro-pyridin-3-ylethynyl)-phenyl]-oxazolidin-2-one; compound with trifluoro-acetic acid
ComponentsTryptase beta-2
KeywordsHYDROLASE / HUMAN TRYPTASE / SERINE PROTEINASE
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-5TA / Tryptase beta-2 / Tryptase alpha/beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsBanner, D. / Benz, J. / Joseph, C. / Kuglstatter, A.
CitationJournal: J.Med.Chem. / Year: 2016
Title: A Real-World Perspective on Molecular Design.
Authors: Kuhn, B. / Guba, W. / Hert, J. / Banner, D. / Bissantz, C. / Ceccarelli, S. / Haap, W. / Korner, M. / Kuglstatter, A. / Lerner, C. / Mattei, P. / Neidhart, W. / Pinard, E. / Rudolph, M.G. / ...Authors: Kuhn, B. / Guba, W. / Hert, J. / Banner, D. / Bissantz, C. / Ceccarelli, S. / Haap, W. / Korner, M. / Kuglstatter, A. / Lerner, C. / Mattei, P. / Neidhart, W. / Pinard, E. / Rudolph, M.G. / Schulz-Gasch, T. / Woltering, T. / Stahl, M.
History
DepositionNov 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Mar 20, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptase beta-2
B: Tryptase beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8514
Polymers54,9832
Non-polymers8682
Water12,412689
1
A: Tryptase beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9252
Polymers27,4911
Non-polymers4341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tryptase beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9252
Polymers27,4911
Non-polymers4341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.340, 78.340, 165.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Tryptase beta-2 / Tryptase-2 / Tryptase II


Mass: 27491.426 Da / Num. of mol.: 2 / Mutation: NO
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: MAST CELLS / Gene: TPSB2, TPS2 / Production host: Komagataella pastoris (fungus) / References: UniProt: P20231, UniProt: Q15661*PLUS, tryptase
#2: Chemical ChemComp-5TA / (5~{S})-5-[[3-(aminomethyl)phenoxy]methyl]-3-[3-[2-(2-chloranylpyridin-3-yl)ethynyl]phenyl]-1,3-oxazolidin-2-one


Mass: 433.887 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H20ClN3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 689 / 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

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG 10000, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.94→67.88 Å / Num. obs: 43956 / % possible obs: 98.8 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.096 / Net I/av σ(I): 13.84 / Net I/σ(I): 0.0103
Reflection shellResolution: 1.94→2.06 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 4.78 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.3.0008refinement
XDSdata reduction
XPREPdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house structure

Resolution: 1.94→67.88 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.787 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20026 2218 5 %RANDOM
Rwork0.15494 ---
obs0.15726 41738 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.628 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20.16 Å20 Å2
2--0.33 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.94→67.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3831 0 62 689 4582
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0214171
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.9565735
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2335508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.51923.511188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03115613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0391525
X-RAY DIFFRACTIONr_chiral_restr0.10.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023325
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.22027
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22808
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2543
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.292
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.240
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.681.52565
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.07424087
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.67531926
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.424.51648
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.944→1.995 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 138 -
Rwork0.192 2906 -
obs--93.52 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.73390.1822-0.27761.3302-0.44720.7634-0.0013-0.0698-0.02870.0795-0.0122-0.07050.01810.06340.0135-0.0926-0.0065-0.0044-0.1341-0.0063-0.1106-21.4239.343-1.269
20.83390.09670.17260.56940.15651.90950.0202-0.0602-0.01960.12070.00260.0020.2216-0.0685-0.0228-0.03810.0012-0.0026-0.15880.0018-0.0904-25.615-28.003-23.88
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 243
2X-RAY DIFFRACTION2B16 - 244

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