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- PDB-6vxy: Triazole bridged SFTI1 inhibitor in complex with beta-trypsin -

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Basic information

Entry
Database: PDB / ID: 6vxy
TitleTriazole bridged SFTI1 inhibitor in complex with beta-trypsin
Components
  • Cationic trypsin
  • SFTI1 inhibitor GLY-ARG-GLY-THR-LYS-SER-ILE-PRO-PRO-ILE-ALA-PHE-PRO-ASP
KeywordsBIOSYNTHETIC PROTEIN / Triazole / Peptidomimetic
Function / homology
Function and homology information


negative regulation of endopeptidase activity / endopeptidase inhibitor activity / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / protease binding / endopeptidase activity / serine-type endopeptidase activity ...negative regulation of endopeptidase activity / endopeptidase inhibitor activity / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / protease binding / 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
cyclic trypsin inhibitor / 1-methyl-1H-1,2,3-triazole / Serine protease 1 / Trypsin inhibitor 1
Similarity search - Component
Biological speciesBos taurus (cattle)
Helianthus annuus (common sunflower)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.398 Å
AuthorsWhite, A.M. / King, G.J. / Durek, T. / Craik, D.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP150100443 Australia
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Application and Structural Analysis of Triazole-Bridged Disulfide Mimetics in Cyclic Peptides.
Authors: White, A.M. / de Veer, S.J. / Wu, G. / Harvey, P.J. / Yap, K. / King, G.J. / Swedberg, J.E. / Wang, C.K. / Law, R.H.P. / Durek, T. / Craik, D.J.
History
DepositionFeb 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cationic trypsin
C: SFTI1 inhibitor GLY-ARG-GLY-THR-LYS-SER-ILE-PRO-PRO-ILE-ALA-PHE-PRO-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9054
Polymers24,7822
Non-polymers1232
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-18 kcal/mol
Surface area9230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.319, 64.861, 70.149
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin
#2: Protein/peptide SFTI1 inhibitor GLY-ARG-GLY-THR-LYS-SER-ILE-PRO-PRO-ILE-ALA-PHE-PRO-ASP


Type: Polypeptide / Class: Trypsin inhibitor / Mass: 1457.673 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Helianthus annuus (common sunflower) / References: cyclic trypsin inhibitor, UniProt: Q4GWU5*PLUS
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-WMH / 1-methyl-1H-1,2,3-triazole


Mass: 83.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 42.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Precipitant: 30% PEG4000, TrisBase (0.1m 8.5 pH), NH4Ac (0.26 M). Protein solution: 22 mg/mL in TrisHCL (0.1M, pH 8.0) with CaCl2 (10 mM). Seeded from trypsin crystals

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.39572→47.6235 Å / Num. obs: 42301 / % possible obs: 98.8462 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.034 / Net I/σ(I): 9
Reflection shellResolution: 1.398→1.42 Å / Rmerge(I) obs: 1.043 / Num. unique obs: 1604

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SFI

1sfi


Resolution: 1.398→33.204 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.84
RfactorNum. reflection% reflection
Rfree0.2447 1992 4.73 %
Rwork0.2123 --
obs0.2139 42134 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.53 Å2 / Biso mean: 28.8927 Å2 / Biso min: 12.14 Å2
Refinement stepCycle: final / Resolution: 1.398→33.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 10 144 1885
Biso mean--27.58 31.12 -
Num. residues----237
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3982-1.43320.36761210.3658252989
1.4332-1.47190.31891400.3282856100
1.4719-1.51520.34471450.31082833100
1.5152-1.56410.31461390.2762862100
1.5641-1.620.30371440.25622859100
1.62-1.68490.28121300.24752851100
1.6849-1.76160.271610.22972844100
1.7616-1.85440.26861370.22592905100
1.8544-1.97060.25811380.21952858100
1.9706-2.12270.23461460.21532897100
2.1227-2.33630.24261530.20742897100
2.3363-2.67430.23161400.20712905100
2.6743-3.36880.23991470.20942962100
3.3688-33.2040.21081510.17313084100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.24130.3741-0.13163.7126-0.82942.7436-0.06640.03590.0642-0.1541-0.0074-0.1554-0.08430.14010.0640.1443-0.0230.01940.13630.00360.1026-2.0074.8795-12.9481
22.2987-0.2523-0.21942.4475-1.02722.31390.0146-0.02780.07290.157-0.0883-0.0729-0.30030.09460.0650.2013-0.01760.01850.0955-0.01890.1082-4.92777.0314-6.741
33.12990.3-0.13333.3206-0.79062.8464-0.0303-0.1147-0.06620.1781-0.0569-0.00240.1097-0.00290.08110.2016-0.00080.02460.1137-0.0070.0821-7.4907-3.7217-1.2495
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 103 )A16 - 103
2X-RAY DIFFRACTION2chain 'A' and (resid 104 through 155 )A104 - 155
3X-RAY DIFFRACTION3chain 'A' and (resid 156 through 245 )A156 - 245

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