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- PDB-8xnj: Crystal structure of trypsin in-complex with arginine -

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Basic information

Entry
Database: PDB / ID: 8xnj
TitleCrystal structure of trypsin in-complex with arginine
ComponentsCationic trypsin
KeywordsHYDROLASE/INHIBITOR / HYDROLASE / trypsin inhibitor / arginine / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / : / 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 / DI(HYDROXYETHYL)ETHER / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAkbar, Z. / Ahmad, M.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Prod Res / Year: 2024
Title: In vitro , in silico and crystallographic-based identification of serine protease inhibitors.
Authors: Akbar, Z. / Ahmad, M.S.
History
DepositionDec 30, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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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)23,7527
Polymers23,3241
Non-polymers4286
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.101, 58.152, 66.288
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, 105 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
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: 1.54 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Apr 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→19.81 Å / Num. obs: 8097 / % possible obs: 99.7 % / Redundancy: 5.3 % / CC1/2: 0.96 / Rrim(I) all: 0.348 / Net I/σ(I): 8.5
Reflection shellResolution: 2.4→2.4 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.708 / Mean I/σ(I) obs: 4 / Num. unique obs: 852 / CC1/2: 0.99 / Rrim(I) all: 0.896 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
PROTEUM PLUSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SY3

6sy3


Resolution: 2.4→19.81 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.852 / SU B: 10.127 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.592 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2749 417 4.9 %RANDOM
Rwork0.19151 ---
obs0.19565 8097 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.915 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å2-0 Å2-0 Å2
2---0.27 Å2-0 Å2
3---1.78 Å2
Refinement stepCycle: 1 / Resolution: 2.4→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1635 0 16 99 1750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121676
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161554
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.762269
X-RAY DIFFRACTIONr_angle_other_deg0.5091.7273595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1685222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.66453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40210268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021982
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02366
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_it0.9711.308894
X-RAY DIFFRACTIONr_mcbond_other0.9571.307894
X-RAY DIFFRACTIONr_mcangle_it1.6242.3421114
X-RAY DIFFRACTIONr_mcangle_other1.6272.3451115
X-RAY DIFFRACTIONr_scbond_it1.4651.412782
X-RAY DIFFRACTIONr_scbond_other1.4651.414783
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3572.5281156
X-RAY DIFFRACTIONr_long_range_B_refined4.23214.621930
X-RAY DIFFRACTIONr_long_range_B_other4.20114.311919
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 24 -
Rwork0.261 587 -
obs--98.07 %

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