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- PDB-6u22: Crystal structure of SFTI-triazole inhibitor in complex with beta... -

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Basic information

Entry
Database: PDB / ID: 6u22
TitleCrystal structure of SFTI-triazole inhibitor in complex with beta-trypsin
Components
  • Cationic trypsin
  • GLY-ARG-ALA-THR-LYS-SER-ILE-PRO-PRO-ILE-ALA-PHE-PRO-ASP
KeywordsHYDROLASE/INHIBITOR / Triazole / Peptidomimetic / BIOSYNTHETIC PROTEIN / HYDROLASE-INHIBITOR complex
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 / endopeptidase activity / protease binding / 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 / endopeptidase activity / protease binding / 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
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: 1.42 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
DepositionAug 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: 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 1.2Oct 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 / struct_conn_type
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,9194
Polymers24,7962
Non-polymers1232
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-19 kcal/mol
Surface area9370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.386, 63.412, 69.517
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 GLY-ARG-ALA-THR-LYS-SER-ILE-PRO-PRO-ILE-ALA-PHE-PRO-ASP


Mass: 1471.699 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Helianthus annuus (common sunflower) / References: 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.: 198 / 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: 2.77 Å3/Da / Density % sol: 55.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Precipitant: PEG4000 (25%-35% w/v), TrisBase (0.1 M, 8.5-9.5 pH) and NH4Ac (0.26 M). Protein solution: 22 mg/mL in Tris.HCl (0.1 M, pH 8.0) with CaCl2 (10 mM)
PH range: 8.5-9.5

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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: Jun 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.42→46.85 Å / Num. obs: 52571 / % possible obs: 99.5 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 18.2
Reflection shellResolution: 1.42→1.44 Å / Rmerge(I) obs: 0.371 / Num. unique obs: 2321

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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: 1.42→37.462 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 15.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1743 1996 3.8 %
Rwork0.1564 50502 -
obs0.1571 52498 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.15 Å2 / Biso mean: 21.3542 Å2 / Biso min: 10.45 Å2
Refinement stepCycle: final / Resolution: 1.42→37.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1732 0 10 198 1940
Biso mean--25.27 30.87 -
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 (%)
1.42-1.45550.22741350.1986334894
1.4555-1.49480.17131370.16543571100
1.4948-1.53880.19211430.15783585100
1.5388-1.58850.16761460.15373602100
1.5885-1.64530.17251400.14713569100
1.6453-1.71110.15831360.14263599100
1.7111-1.7890.14821480.15013577100
1.789-1.88330.16081410.15383601100
1.8833-2.00130.16711390.14983609100
2.0013-2.15580.1671440.14743612100
2.1558-2.37280.161450.15273629100
2.3728-2.7160.16251460.15493666100
2.716-3.42150.19521400.16513690100
3.4215-37.4620.18061560.15843844100
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)
11.1350.1754-0.51151.4299-0.30441.3283-0.0189-0.02590.00370.03380.01630.03520.0152-0.0534-0.00030.0935-0.0021-0.00370.0938-0.00730.0879-8.7060.299-7.898
25.40432.8868-0.2175.87531.0689.8035-0.07560.2122-0.4743-0.04370.2140.39580.8831-0.6975-0.13450.2093-0.0581-0.01450.2020.00870.2161-19.107-9.17-14.399
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 16:245 )A16 - 245
2X-RAY DIFFRACTION2( CHAIN C AND ( RESID 1:14 OR RESID 101:101 ) )C1 - 14
3X-RAY DIFFRACTION2( CHAIN C AND ( RESID 1:14 OR RESID 101:101 ) )C101

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