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- PDB-9kk4: Crystal Structure of Bovine Pancreatic Trypsin in Complex with Py... -

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Basic information

Entry
Database: PDB / ID: 9kk4
TitleCrystal Structure of Bovine Pancreatic Trypsin in Complex with Pyridoxine
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
4,5-bis(hydroxymethyl)-2-methyl-pyridin-3-ol / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsAkbar, Z. / Ahmad, M.S.
Funding support Pakistan, 1items
OrganizationGrant numberCountry
Not funded Pakistan
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: The in vitro and crystallographic studies reveal the inhibitory potential of vitamin B 6 analogues against a serine protease trypsin.
Authors: Akbar, Z. / Shah, N. / Mirza, S. / Rasheed, S. / Ahmad, M.S.
History
DepositionNov 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7897
Polymers23,3241
Non-polymers4646
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-26 kcal/mol
Surface area8930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.045, 57.750, 65.676
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 , 5 types, 135 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-UEG / 4,5-bis(hydroxymethyl)-2-methyl-pyridin-3-ol


Mass: 169.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES (pH =7.5), 0.1-0.4 M Li2SO4, and PEG 16%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 VENTURE / Wavelength: 1.5406 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Mar 12, 2021
RadiationMonochromator: Ni / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.35→19.74 Å / Num. obs: 8986 / % possible obs: 99.7 % / Redundancy: 6.8 % / Rrim(I) all: 0.183 / Net I/σ(I): 11.2
Reflection shellResolution: 2.35→2.44 Å / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 5.4 / Num. unique obs: 922

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
PROTEUM PLUSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SY3

6sy3


Resolution: 2.35→19.74 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.856 / SU B: 8.348 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.566 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26006 450 5 %RANDOM
Rwork0.19903 ---
obs0.20208 8502 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.572 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å2-0 Å2
2--0.36 Å20 Å2
3----0.55 Å2
Refinement stepCycle: 1 / Resolution: 2.35→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1641 0 15 129 1785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121704
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161568
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.7512311
X-RAY DIFFRACTIONr_angle_other_deg0.5061.7253629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9575224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.7352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77410270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0650.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022001
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02365
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_it1.0071.537896
X-RAY DIFFRACTIONr_mcbond_other1.0071.537896
X-RAY DIFFRACTIONr_mcangle_it1.7072.761120
X-RAY DIFFRACTIONr_mcangle_other1.7072.761121
X-RAY DIFFRACTIONr_scbond_it1.071.612808
X-RAY DIFFRACTIONr_scbond_other1.0691.612809
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8242.911192
X-RAY DIFFRACTIONr_long_range_B_refined3.43316.852101
X-RAY DIFFRACTIONr_long_range_B_other3.43316.852102
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 38 -
Rwork0.192 602 -
obs--100 %

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