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

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Basic information

Entry
Database: PDB / ID: 3uuz
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 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-0CB / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Dec 5, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Sep 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_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_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cationic trypsin
B: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2819
Polymers46,8492
Non-polymers1,4327
Water10,683593
1
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0944
Polymers23,4241
Non-polymers6703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1865
Polymers23,4241
Non-polymers7624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.460, 77.850, 171.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 23424.406 Da / Num. of mol.: 2
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) / Strain (production host): BL21(DE3) / References: UniProt: P00760, trypsin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-0CB / {[(7-carbamimidoylnaphthalen-2-yl)methyl][4-({1-[(1E)-ethanimidoyl]piperidin-4-yl}oxy)phenyl]sulfamoyl}acetic acid


Mass: 537.631 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H31N5O5S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 593 / Source method: isolated from a natural source / Formula: H2O

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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: 2.66 Å3/Da / Density % sol: 53.71 %
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: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Rmerge(I) obs: 0.08 / Net I/σ(I): 36.6

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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: 2.1→28.96 Å / Cor.coef. Fo:Fc: 0.958 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflectionSelection details
Rfree0.19997 1456 RANDOM
Rwork0.14375 --
all0.14875 29112 -
obs0.14875 29112 -
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.772 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3274 0 96 593 3963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0530.0223466
X-RAY DIFFRACTIONr_angle_refined_deg1.771.9744699
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1595444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82825.593118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6915548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.788154
X-RAY DIFFRACTIONr_chiral_restr0.0830.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212542
X-RAY DIFFRACTIONr_mcbond_it3.6421.52205
X-RAY DIFFRACTIONr_mcangle_it4.38523522
X-RAY DIFFRACTIONr_scbond_it5.56131261
X-RAY DIFFRACTIONr_scangle_it6.5854.51172

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