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- PDB-2bm2: human beta-II tryptase in complex with 4-(3-Aminomethyl-phenyl)- ... -

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Basic information

Entry
Database: PDB / ID: 2bm2
Titlehuman beta-II tryptase in complex with 4-(3-Aminomethyl-phenyl)- piperidin-1-yl-(5-phenethyl- pyridin-3-yl)-methanone
ComponentsHUMAN BETA2 TRYPTASE
KeywordsHYDROLASE / SERINE PROTEASE INHIBITOR / GLYCOPROTEIN / POLYMORPHISM / PROTEASE / SERINE PROTEASE
Function / homology
Function and homology information


tryptase / serine-type peptidase activity / collagen-containing extracellular matrix / serine-type endopeptidase activity / proteolysis / extracellular space
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-PM2 / Tryptase beta-2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMaignan, S. / Guilloteau, J.-P. / Dupuy, A. / Levell, J. / Astles, P. / Eastwood, P. / Cairns, J. / Houille, O. / Aldous, S. / Merriman, G. ...Maignan, S. / Guilloteau, J.-P. / Dupuy, A. / Levell, J. / Astles, P. / Eastwood, P. / Cairns, J. / Houille, O. / Aldous, S. / Merriman, G. / Whiteley, B. / Pribish, J. / Czekaj, M. / Liang, G. / Davidson, J. / Harrison, T. / Morley, A. / Watson, S. / Fenton, G. / Mccarthy, C. / Romano, J. / Mathew, R. / Engers, D. / Gardyan, M. / Sides, K. / Kwong, J. / Tsay, J. / Rebello, S. / Shen, L. / Wang, J. / Luo, Y. / Giardino, O. / Lim, H.-K. / Smith, K. / Pauls, H.
CitationJournal: Bioorg.Med.Chem. / Year: 2005
Title: Structure Based Design of 4-(3-Aminomethylphenyl) Piperidinyl-1-Amides: Novel, Potent, Selective, and Orally Bioavailable Inhibitors of Bii Tryptase
Authors: Levell, J. / Astles, P. / Eastwood, P. / Cairns, J. / Houille, O. / Aldous, S. / Merriman, G. / Whitley, B. / Pribish, J. / Czekaj, M. / Liang, G. / Maignan, S. / Guilloteau, J.-P. / Dupuy, ...Authors: Levell, J. / Astles, P. / Eastwood, P. / Cairns, J. / Houille, O. / Aldous, S. / Merriman, G. / Whitley, B. / Pribish, J. / Czekaj, M. / Liang, G. / Maignan, S. / Guilloteau, J.-P. / Dupuy, A. / Davidson, J. / Harrison, T. / Morley, A. / Watson, S. / Fenton, G. / Mccarthy, C. / Romano, J. / Mathew, R. / Engers, D. / Gardyan, M. / Sides, K. / Kwong, J. / Tsay, J. / Rebello, S. / Shen, L. / Wang, J. / Luo, Y. / Giardino, O. / Lim, H.-K. / Smith, K. / Pauls, H.
History
DepositionMar 9, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUMAN BETA2 TRYPTASE
B: HUMAN BETA2 TRYPTASE
C: HUMAN BETA2 TRYPTASE
D: HUMAN BETA2 TRYPTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,5648
Polymers109,9664
Non-polymers1,5984
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)82.000, 82.000, 171.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.97483, -0.00822, 0.22281), (0.006, -0.99993, -0.01066), (0.22288, -0.00905, 0.9748)47.24405, 38.386, -4.3492
2given(-0.96382, 0.26628, 0.01239), (0.26628, 0.96389, -0.00221), (-0.01253, 0.00117, -0.99992)39.67802, -5.31754, 0.671
3given(0.94349, -0.247, -0.22094), (-0.25164, -0.96779, 0.00735), (-0.21564, 0.04866, -0.97526)45.32941, 43.31, 4.121

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Components

#1: Protein
HUMAN BETA2 TRYPTASE / TRYPTASE 2 / TRYPTASE II


Mass: 27491.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: DEGLYCOSYLATED PROTEIN / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P20231, tryptase
#2: Chemical
ChemComp-PM2 / 1-[3-(1-{[5-(2-PHENYLETHYL)PYRIDIN-3-YL]CARBONYL}PIPERIDIN-4-YL)PHENYL]METHANAMINE / [4-(3-AMINOMETHYL-PHENYL)-PIPERIDIN-1-YL]-(5-PHENETHYL- PYRIDIN-3-YL)-METHANONE


Mass: 399.528 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H29N3O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: MAJOR NEUTRAL PROTEASE PRESENT IN MAST CELLS

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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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 291 K
Details: PEG 3000 13-19%. NA.ACETATE 100 MM PH 5. T=18 DEG C. TAKES ABOUT 3 DAYS TO GET 200 MICROMETRE SILEX SHAPED CRYSTALS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 51879 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.5 / % possible all: 94.2

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Processing

Software
NameVersionClassification
X-PLOR981refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A0L

1a0l


Resolution: 2.2→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: FREE R-VALUE / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.259 -5 %RANDOM
Rwork0.203 ---
obs0.203 51827 91 %-
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7648 0 120 377 8145
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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