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- PDB-8kdu: Crystal structure of trypsin with its substrate -

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Basic information

Entry
Database: PDB / ID: 8kdu
TitleCrystal structure of trypsin with its substrate
ComponentsCationic trypsin
KeywordsHYDROLASE
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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
ARGININE / ETHANOL / GUANIDINE / : / : / DI(HYDROXYETHYL)ETHER / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAkbar, Z. / Ahmad, M.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Chin Chem Soc / Year: 2024
Title: Crystal structure of the Michaelis complex of trypsin with N-alpha-benzoyl-l-arginine ethyl ester
Authors: Akbar, Z. / Ahmad, M.S.
History
DepositionAug 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)24,58413
Polymers23,3241
Non-polymers1,26012
Water3,405189
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.116, 131.116, 71.424
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-304-

GAI

21A-304-

GAI

31A-444-

HOH

41A-529-

HOH

51A-544-

HOH

61A-555-

HOH

71A-568-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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 (domestic cattle) / References: UniProt: P00760, trypsin

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Non-polymers , 10 types, 201 molecules

#2: Chemical ChemComp-I4Q / ethyl (2~{S})-2-benzamido-5-carbamimidamido-pentanoate


Mass: 306.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-JNR / (2~{R})-2-benzamido-5-carbamimidamido-pentanoic acid


Mass: 278.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H18N4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#5: Chemical ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH5N3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.1 M HEPES (pH=7.8), 16% PEG 3350, and 0.1-0.4 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.6406 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Mar 10, 2021
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6406 Å / Relative weight: 1
ReflectionResolution: 2.3→16.83 Å / Num. obs: 10553 / % possible obs: 99.7 % / Redundancy: 5.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.096 / Net I/σ(I): 19.2
Reflection shellResolution: 2.3→2.3 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 11.2 / Num. unique obs: 1083 / CC1/2: 0.95 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PROTEUM PLUSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SY3

6sy3


Resolution: 2.3→16.83 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.061 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.304 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19782 542 5.1 %RANDOM
Rwork0.1456 ---
obs0.14833 10005 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.216 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.3→16.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 80 189 1898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131731
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151619
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.6292330
X-RAY DIFFRACTIONr_angle_other_deg1.3141.5863734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8485216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.01623.93966
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3215272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.117153
X-RAY DIFFRACTIONr_chiral_restr0.0760.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021960
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02378
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9141.068888
X-RAY DIFFRACTIONr_mcbond_other0.8971.063887
X-RAY DIFFRACTIONr_mcangle_it1.5311.5821096
X-RAY DIFFRACTIONr_mcangle_other1.5391.5861097
X-RAY DIFFRACTIONr_scbond_it1.5111.382839
X-RAY DIFFRACTIONr_scbond_other1.511.384840
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4491.9661229
X-RAY DIFFRACTIONr_long_range_B_refined4.78314.1691990
X-RAY DIFFRACTIONr_long_range_B_other4.78214.1831991
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 42 -
Rwork0.143 726 -
obs--100 %

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