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- PDB-7jwx: Crystal Structure of Trypsin Bound O-methyl Benzamidine -

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Basic information

Entry
Database: PDB / ID: 7jwx
TitleCrystal Structure of Trypsin Bound O-methyl Benzamidine
ComponentsCationic trypsin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Hydrolase inhibitor / HYDROLASE / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Chem-VN1 / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsPackianathan, C. / Laganowsky, A.
CitationJournal: Org.Biomol.Chem. / Year: 2022
Title: Small molecule peptidomimetic trypsin inhibitors: validation of an EKO binding mode, but with a twist.
Authors: Lyu, R.L. / Joy, S. / Packianathan, C. / Laganowsky, A. / Burgess, K.
History
DepositionAug 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)95,82719
Polymers93,2974
Non-polymers2,53015
Water8,071448
1
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9164
Polymers23,3241
Non-polymers5923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8554
Polymers23,3241
Non-polymers5313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0125
Polymers23,3241
Non-polymers6884
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0446
Polymers23,3241
Non-polymers7195
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)189.270, 70.320, 137.740
Angle α, β, γ (deg.)90.000, 133.000, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin

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Non-polymers , 6 types, 463 molecules

#2: Chemical
ChemComp-VN1 / 4-[(1-{(1S,2S)-1-[1-(4-aminobutyl)-1H-1,2,3-triazol-4-yl]-2-methylbutyl}-1H-1,2,3-triazol-4-yl)methoxy]-3-methoxybenzene-1-carboximidamide


Mass: 455.557 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H33N9O2
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.59 Å3/Da / Density % sol: 65.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.9M (NH4)2 SO4, 50mM MES pH 6.0, 2mM O-methyl Benzamidine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS IV / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 27, 2020 / Details: Mirror
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.38→40 Å / Num. obs: 52631 / % possible obs: 98.51 % / Redundancy: 3.07 % / Biso Wilson estimate: 27.52 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.08 / Net I/σ(I): 13.4
Reflection shellResolution: 2.38→2.46 Å / Redundancy: 2.85 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 4 / Num. unique obs: 3703 / CC1/2: 0.928 / Rrim(I) all: 0.33 / % possible all: 93.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F2S

1f2s


Resolution: 2.38→38.58 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2554 2632 5 %
Rwork0.2119 49985 -
obs0.2141 52617 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.28 Å2 / Biso mean: 29.0329 Å2 / Biso min: 12.77 Å2
Refinement stepCycle: final / Resolution: 2.38→38.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6516 0 164 448 7128
Biso mean--29.68 31.12 -
Num. residues----892
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.38-2.420.34731270.27812415254290
2.42-2.470.34561360.2572572270898
2.47-2.520.26731370.24162617275499
2.52-2.580.2921370.23952594273199
2.58-2.630.3271380.23672625276399
2.63-2.70.27081390.2432635277499
2.7-2.770.30351380.24282630276899
2.77-2.860.35011380.24822613275199
2.86-2.950.2791380.24062634277299
2.95-3.050.25311400.23482665280599
3.05-3.180.24941390.21332629276899
3.18-3.320.26161390.21892642278199
3.32-3.490.26971400.216726562796100
3.49-3.710.22921400.20126562796100
3.71-40.25441390.18726442783100
4-4.40.19711420.1712698284099
4.4-5.040.21221400.17732664280499
5.04-6.340.24271410.20512678281999
6.34-38.580.21761440.20092718286298

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