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

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Basic information

Entry
Database: PDB / ID: 3uop
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 / 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
N~2~-(BENZYLSULFONYL)-D-ARGINYL-N-(4-CARBAMIMIDOYLBENZYL)GLYCINAMIDE / DI(HYDROXYETHYL)ETHER / Chem-PMJ / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.69 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 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Non-polymer description
Revision 1.2Jul 16, 2014Group: Database references
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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 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)24,3978
Polymers23,4101
Non-polymers9867
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.089, 55.089, 154.868
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-1331-

HOH

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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: 23410.379 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 (domestic cattle) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: P00760, trypsin

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Non-polymers , 6 types, 349 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PMJ / N~2~-(benzylsulfonyl)-D-arginyl-N-(4-carbamimidoylbenzyl)glycinamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 516.616 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H32N8O4S
References: N~2~-(BENZYLSULFONYL)-D-ARGINYL-N-(4-CARBAMIMIDOYLBENZYL)GLYCINAMIDE
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.9 Å3/Da / Density % sol: 57.55 %
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: 1.69→35.04 Å / Num. all: 28059 / Num. obs: 28059 / % possible obs: 88.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 5.6 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 12.6
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 2.5 / % possible all: 24

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
d*TREKdata reduction
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V2K

1v2k


Resolution: 1.69→35.04 Å / Cor.coef. Fo:Fc: 0.961 / WRfactor Rwork: 0.1776 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8967 / SU R Cruickshank DPI: 0.1008 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22001 2210 -RANDOM
Rwork0.18037 ---
all0.1856 28058 --
obs0.1856 28058 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 72.65 Å2 / Biso mean: 23.5569 Å2 / Biso min: 10.49 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20.54 Å20 Å2
2--1.08 Å20 Å2
3----1.62 Å2
Refinement stepCycle: LAST / Resolution: 1.69→35.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 60 342 2038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221752
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.9712382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4675230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37325.59359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.76115277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.267152
X-RAY DIFFRACTIONr_chiral_restr0.1010.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211297
X-RAY DIFFRACTIONr_mcbond_it0.6841.51113
X-RAY DIFFRACTIONr_mcangle_it1.20921789
X-RAY DIFFRACTIONr_scbond_it1.9853639
X-RAY DIFFRACTIONr_scangle_it2.9194.5590
LS refinement shellResolution: 1.686→1.73 Å / Rfactor Rfree error: 0.418 / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.463 15
Rwork0.424 421
obs-421

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