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- PDB-3upe: Bovine trypsin variant X(triplePhe227) in complex with small mole... -

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Basic information

Entry
Database: PDB / ID: 3upe
TitleBovine trypsin variant X(triplePhe227) in complex with small molecule inhibitor
ComponentsCationic trypsin
KeywordsHYDROLASE/HYDROLASE inhibitor / Trypsin-like serine protease / HYDROLASE / 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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-0CA / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.54 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 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Sep 13, 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_asym_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_asym_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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 1.3Oct 9, 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: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2746
Polymers23,4241
Non-polymers8505
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.644, 54.644, 154.887
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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: 23424.406 Da / Num. of mol.: 1
Mutation: N102E, L104Y, Y175S, P176S, G177F, Q178Y, S195A, V228F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: P00760, trypsin

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Non-polymers , 5 types, 384 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-0CA / 1-[(7-carbamimidoylnaphthalen-2-yl)methyl]-6-({1-[(1Z)-ethanimidoyl]piperidin-4-yl}oxy)-2-(propan-2-yl)-1H-indole-4-carboxylic acid


Mass: 525.641 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H35N5O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.85 Å3/Da / Density % sol: 56.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG8000, 0.1M AMMONIUM SULPHATE, 0.1M IMIDAZOLE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. all: 32874 / Num. obs: 32874 / % possible obs: 81 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 5.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.7
Reflection shellResolution: 1.54→1.59 Å / Redundancy: 1.56 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 2.8 / % possible all: 22

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0109refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V2K

1v2k


Resolution: 1.54→45.26 Å / Cor.coef. Fo:Fc: 0.954 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21883 1694 -RANDOM
Rwork0.19024 ---
all0.19064 32874 --
obs0.19064 32852 81.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.572 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å20 Å2
2--0.03 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.54→45.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1637 0 56 379 2072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221790
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.431.9782450
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5125241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.85625.64562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.20315283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.301152
X-RAY DIFFRACTIONr_chiral_restr0.1150.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211350
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7751.51134
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.34821828
X-RAY DIFFRACTIONr_scbond_it2.0753656
X-RAY DIFFRACTIONr_scangle_it3.194.5614
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.543→1.583 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.61 35 -
Rwork0.548 602 -
obs-602 20.46 %

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