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- PDB-3pwb: Bovine trypsin variant X(tripleGlu217Ile227) in complex with smal... -

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Basic information

Entry
Database: PDB / ID: 3pwb
TitleBovine trypsin variant X(tripleGlu217Ile227) in complex with small molecule inhibitor
ComponentsCationic trypsin
KeywordsHYDROLASE / trypsin-like serine protease / protein binding / duodenum
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 / MOLECULAR REPLACEMENT / Resolution: 1.63 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
DepositionDec 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Sep 24, 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 / 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 1.4Nov 6, 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)23,7675
Polymers23,4181
Non-polymers3484
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.567, 54.567, 106.512
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1214-

HOH

21A-1252-

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: 23418.398 Da / Num. of mol.: 1 / Fragment: UNP residues 24-246
Mutation: N102E, L104Y, Y175S, P176S, G177F, Q178I, S195A, S218E, 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, 426 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / 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.: 422 / 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: 1.95 Å3/Da / Density % sol: 37.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% PEG8000, 0.1M AMMONIUM SULPHATE, 0.1M IMIDAZOLE, pH 7.0, 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: 1.63→20 Å / Num. all: 23624 / Num. obs: 23624 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 10.6
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 6.64 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
PHENIX(phenix.refine: 1.5_2)refinement
d*TREKdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V2K

1v2k


Resolution: 1.63→20 Å / SU ML: 0.25 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2102 2325 10 %RANDOM
Rwork0.1567 ---
all0.1599 23582 --
obs0.1599 23582 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.406 Å2 / ksol: 0.343 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.5756 Å20 Å20 Å2
2---0.5756 Å2-0 Å2
3---1.1511 Å2
Refinement stepCycle: LAST / Resolution: 1.63→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 21 422 2079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081702
X-RAY DIFFRACTIONf_angle_d1.1822299
X-RAY DIFFRACTIONf_dihedral_angle_d17.891590
X-RAY DIFFRACTIONf_chiral_restr0.08257
X-RAY DIFFRACTIONf_plane_restr0.005293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.64850.30437600.3043760X-RAY DIFFRACTION100
1.6485-1.66790.28787580.2878758X-RAY DIFFRACTION100
1.6679-1.68830.28447970.2844797X-RAY DIFFRACTION100
1.6883-1.70960.26327790.2632779X-RAY DIFFRACTION100
1.7096-1.73210.2637370.263737X-RAY DIFFRACTION100
1.7321-1.75580.23978000.2397800X-RAY DIFFRACTION100
1.7558-1.78090.24127490.2412749X-RAY DIFFRACTION100
1.7809-1.80740.21327830.2132783X-RAY DIFFRACTION100
1.8074-1.83570.19697860.1969786X-RAY DIFFRACTION100
1.8357-1.86570.1757640.175764X-RAY DIFFRACTION100
1.8657-1.89790.16337920.1633792X-RAY DIFFRACTION100
1.8979-1.93240.17547700.1754770X-RAY DIFFRACTION100
1.9324-1.96950.14127750.1412775X-RAY DIFFRACTION100
1.9695-2.00970.12197840.1219784X-RAY DIFFRACTION100
2.0097-2.05330.12587630.1258763X-RAY DIFFRACTION100
2.0533-2.1010.13867950.1386795X-RAY DIFFRACTION100
2.101-2.15350.14027690.1402769X-RAY DIFFRACTION100
2.1535-2.21170.13547730.1354773X-RAY DIFFRACTION100
2.2117-2.27670.12658000.1265800X-RAY DIFFRACTION100
2.2767-2.350.12327700.1232770X-RAY DIFFRACTION100
2.35-2.43390.13437840.1343784X-RAY DIFFRACTION100
2.4339-2.53110.14687840.1468784X-RAY DIFFRACTION100
2.5311-2.64610.15387950.1538795X-RAY DIFFRACTION100
2.6461-2.78520.13868010.1386801X-RAY DIFFRACTION100
2.7852-2.95920.1387970.138797X-RAY DIFFRACTION100
2.9592-3.18680.12777900.1277790X-RAY DIFFRACTION100
3.1868-3.50580.12368030.1236803X-RAY DIFFRACTION100
3.5058-4.00940.11958180.1195818X-RAY DIFFRACTION100
4.0094-5.03730.11668210.1166821X-RAY DIFFRACTION100
5.0373-19.67180.16768850.1676885X-RAY DIFFRACTION100

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