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- PDB-3plb: Bovine trypsin variant X(tripleIle227) in complex with small mole... -

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Basic information

Entry
Database: PDB / ID: 3plb
TitleBovine trypsin variant X(tripleIle227) in complex with small molecule inhibitor
ComponentsCationic trypsin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Trypsin-like serine protease / PROTEIN BINDING / DUODENUM / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion 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 ...: / 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
BENZAMIDINE / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsTziridis, A. / Neumann, P. / Kolenko, P. / Stubbs, M.T.
CitationJournal: Biol.Chem. / Year: 2014
Title: Correlating structure and ligand affinity in drug discovery: a cautionary tale involving second shell residues.
Authors: Tziridis, A. / Rauh, D. / Neumann, P. / Kolenko, P. / Menzel, A. / Brauer, U. / Ursel, C. / Steinmetzer, P. / Sturzebecher, J. / Schweinitz, A. / Steinmetzer, T. / Stubbs, M.T.
History
DepositionNov 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Sep 24, 2014Group: Database references
Revision 1.3Sep 6, 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 / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 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: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8176
Polymers23,3761
Non-polymers4405
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.727, 54.727, 107.998
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cationic trypsin / Beta-trypsin / Alpha-trypsin chain 1 / Alpha-trypsin chain 2


Mass: 23376.363 Da / Num. of mol.: 1 / Fragment: UNP residues 24-246
Mutation: N102E, L104Y, Y175S, P176S, G177F, Q178Y, S195A, V228I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: P00760, trypsin

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Non-polymers , 5 types, 395 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O

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Details

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 Å3/Da / Density % sol: 38.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 8000, 0.1M imidazole, 0.3M ammonium sulphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.18→20 Å / Num. all: 60207 / Num. obs: 60207 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19 % / Biso Wilson estimate: 10.7 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 19.1

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Processing

Software
NameVersionClassification
MxCuBEdata collection
AMoREphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V2K

1v2k


Resolution: 1.18→20 Å / SU ML: 0.12 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1477 6096 100 %RANDOM
Rwork0.1291 ---
all0.1298 60207 --
obs0.1298 60207 97.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.4 e/Å3
Refinement stepCycle: LAST / Resolution: 1.18→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1633 0 27 390 2050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071752
X-RAY DIFFRACTIONf_angle_d1.2512379
X-RAY DIFFRACTIONf_dihedral_angle_d17.403623
X-RAY DIFFRACTIONf_chiral_restr0.085267
X-RAY DIFFRACTIONf_plane_restr0.006304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1828-1.19620.208219200.20821920X-RAY DIFFRACTION94
1.1962-1.21030.19719800.1971980X-RAY DIFFRACTION98
1.2103-1.2250.188319770.18831977X-RAY DIFFRACTION98
1.225-1.24050.170720050.17072005X-RAY DIFFRACTION97
1.2405-1.25680.170619770.17061977X-RAY DIFFRACTION98
1.2568-1.2740.153220100.15322010X-RAY DIFFRACTION98
1.274-1.29220.152519830.15251983X-RAY DIFFRACTION98
1.2922-1.31150.141619630.14161963X-RAY DIFFRACTION97
1.3115-1.3320.125420260.12542026X-RAY DIFFRACTION97
1.332-1.35380.124719760.12471976X-RAY DIFFRACTION98
1.3538-1.37720.115320010.11532001X-RAY DIFFRACTION98
1.3772-1.40220.105819750.10581975X-RAY DIFFRACTION97
1.4022-1.42910.105819880.10581988X-RAY DIFFRACTION98
1.4291-1.45830.097220180.09722018X-RAY DIFFRACTION98
1.4583-1.490.087119880.08711988X-RAY DIFFRACTION98
1.49-1.52460.08420210.0842021X-RAY DIFFRACTION98
1.5246-1.56270.083920310.08392031X-RAY DIFFRACTION99
1.5627-1.60490.084820260.08482026X-RAY DIFFRACTION99
1.6049-1.65210.088220400.08822040X-RAY DIFFRACTION99
1.6521-1.70540.096220410.09622041X-RAY DIFFRACTION99
1.7054-1.76620.100920280.10092028X-RAY DIFFRACTION98
1.7662-1.83690.106420150.10642015X-RAY DIFFRACTION98
1.8369-1.92030.111320000.11132000X-RAY DIFFRACTION97
1.9203-2.02140.109320190.10932019X-RAY DIFFRACTION96
2.0214-2.14770.116119970.11611997X-RAY DIFFRACTION97
2.1477-2.31310.12120470.1212047X-RAY DIFFRACTION98
2.3131-2.5450.130520290.13052029X-RAY DIFFRACTION97
2.545-2.91130.142720280.14272028X-RAY DIFFRACTION96
2.9113-3.66030.128520190.12852019X-RAY DIFFRACTION94
3.6603-15.79970.141720790.14172079X-RAY DIFFRACTION93

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