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- PDB-6bvh: Trypsin complexed with a modified sunflower trypsin inhibitor, SF... -

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Basic information

Entry
Database: PDB / ID: 6bvh
TitleTrypsin complexed with a modified sunflower trypsin inhibitor, SFTI-TCTR(N12,N14)
Components
  • Cationic trypsin
  • Trypsin inhibitor 1
KeywordsHYDROLASE/INHIBITOR / Protease inhibitor complex / sunflower trypsin inhibitor / sfti / HYDROLASE / 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 / 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 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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
Serine protease 1 / Trypsin inhibitor 1
Similarity search - Component
Biological speciesBos taurus (cattle)
Helianthus annuus (common sunflower)
MethodX-RAY DIFFRACTION / Resolution: 1.927 Å
AuthorsRiley, B.T. / Chen, X.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health & Medical Research Council1059410 Australia
CitationJournal: PLoS ONE / Year: 2019
Title: Potent, multi-target serine protease inhibition achieved by a simplified beta-sheet motif.
Authors: Chen, X. / Riley, B.T. / de Veer, S.J. / Hoke, D.E. / Van Haeften, J. / Leahy, D. / Swedberg, J.E. / Brattsand, M. / Hartfield, P.J. / Buckle, A.M. / Harris, J.M.
History
DepositionDec 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cationic trypsin
I: Trypsin inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,49510
Polymers24,7982
Non-polymers6978
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-55 kcal/mol
Surface area9330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.680, 63.240, 69.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AI

#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 Trypsin inhibitor 1


Mass: 1473.697 Da / Num. of mol.: 1
Mutation: R2T, K4R, F12N, D14N compared to UNP Q4GWU5, residues 40-53
Source method: obtained synthetically / Details: Cyclic peptide / Source: (synth.) Helianthus annuus (common sunflower) / References: UniProt: Q4GWU5*PLUS

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Non-polymers , 4 types, 368 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 50 mM MES, 50 mM benzamidine, 1mM CaCl2

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen vapor stream
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.927→63.24 Å / Num. obs: 20647 / % possible obs: 98 % / Redundancy: 3.6 % / Biso Wilson estimate: 13.74 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.021 / Rrim(I) all: 0.041 / Net I/σ(I): 27.1
Reflection shellResolution: 1.93→1.97 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.063 / Num. unique obs: 1331 / CC1/2: 0.993 / Rpim(I) all: 0.04 / Rrim(I) all: 0.075 / % possible all: 95.2

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Processing

Software
NameVersionClassification
MOSFLM7.2.0data reduction
Aimless0.5.12data scaling
PHENIX1.13rc1refinement
PDB_EXTRACT3.24data extraction
RefinementResolution: 1.927→34.66 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 14.4
RfactorNum. reflection% reflection
Rfree0.1582 1112 5.41 %
Rwork0.1319 --
obs0.1334 20647 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.56 Å2 / Biso mean: 18.451 Å2 / Biso min: 4.83 Å2
Refinement stepCycle: final / Resolution: 1.927→34.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1729 0 40 360 2129
Biso mean--38.66 33.1 -
Num. residues----237
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.927-1.97180.1491200.13232412253295
1.9718-2.02110.14541120.12322388250096
2.0211-2.07580.17831500.1192411256196
2.0758-2.13680.15071460.11972407255397
2.1368-2.20580.14841360.12232421255797
2.2058-2.28460.18611240.12892463258797
2.2846-2.37610.14871300.12642435256598
2.3761-2.48420.17561470.12862440258798
2.4842-2.61510.16671640.13342432259698
2.6151-2.77890.16121550.14682437259299
2.7789-2.99340.17341230.14152482260599
2.9934-3.29440.16221360.12782512264899
3.2944-3.77060.13811520.120524462598100
3.7706-4.74860.12771390.11424942633100
4.7486-34.66560.18941610.180824782639100
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)
11.3534-0.05360.42471.9188-0.21651.4546-0.0162-0.046-0.05750.10880.0386-0.1049-0.01410.0156-0.01820.05110.0028-0.00320.0634-0.00260.052526.312228.393813.9953
23.5928-1.41491.9873.1196-1.51564.15590.07640.2009-0.0883-0.28470.0202-0.11520.12440.1043-0.08390.094-0.0050.02670.118-0.03450.061528.322627.3653-1.2869
32.37090.03030.17733.0663-0.34322.947-0.0391-0.2226-0.10660.13860.02490.34430.017-0.41880.01230.0674-0.0196-0.0140.11960.02150.114212.432124.17319.602
44.03234.0016-0.23197.7053-4.04835.9666-0.05070.0601-0.1282-0.51810.0393-0.06540.0398-0.02510.00110.09020.0022-0.02260.10280.00090.055715.292932.7588-5.4164
59.5449-4.7016-2.81338.25542.60217.92040.00580.20840.3576-0.3054-0.1779-0.1924-0.54550.14080.16130.2406-0.0016-0.12650.08670.02120.196812.652444.7149-5.1464
61.8901-0.17140.65652.058-0.68181.1552-0.09440.01580.0936-0.06390.01640.0752-0.2542-0.17210.05180.11580.0225-0.01940.0887-0.01630.057115.993835.8422.6521
73.35830.2891-1.07634.3315-3.55984.8812-0.0561-0.00660.4515-0.17240.13250.7591-0.1276-0.4024-0.08760.13210.1244-0.05040.2963-0.00130.1983.406536.60871.9663
85.58540.60671.65151.5480.20951.9402-0.19650.24270.2299-0.18970.1747-0.2197-0.25250.20640.03070.1367-0.02690.02470.057-0.01610.120731.061138.97874.7431
93.93162.52140.07723.32710.25874.4341-0.0376-0.12780.3398-0.04470.08930.6182-0.489-0.4614-0.06010.14790.084-0.01970.16390.0040.124212.037438.348512.0966
106.51290.00720.33394.404-0.80873.7344-0.13180.1580.76-0.2464-0.04040.3452-0.5148-0.51260.15160.24370.1268-0.04270.2695-0.0430.184811.016341.070116.0415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 16:114)A16 - 114
2X-RAY DIFFRACTION2(chain A and resid 115:135)A115 - 135
3X-RAY DIFFRACTION3(chain A and resid 136:158)A136 - 158
4X-RAY DIFFRACTION4(chain A and resid 159:164)A159 - 164
5X-RAY DIFFRACTION5(chain A and resid 165:170)A165 - 170
6X-RAY DIFFRACTION6(chain A and resid 171:220)A171 - 220
7X-RAY DIFFRACTION7(chain A and resid 221:224)A221 - 224
8X-RAY DIFFRACTION8(chain A and resid 225:245)A225 - 245
9X-RAY DIFFRACTION9(chain I and resid 1:6)I1 - 6
10X-RAY DIFFRACTION10(chain I and resid 7:14)I7 - 14

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