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- PDB-8iyv: Crystal structure of trypsin-famotidine complex at 2.10 Angstroms... -

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Basic information

Entry
Database: PDB / ID: 8iyv
TitleCrystal structure of trypsin-famotidine complex at 2.10 Angstroms resolution
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
famotidine / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAhmad, M.S. / Kalam, N. / Akbar, Z. / Rasheed, S. / Choudhary, M.I.
Funding support Pakistan, 1items
OrganizationGrant numberCountry
Not funded Pakistan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Structural basis for the binding of famotidine, cimetidine, guanidine, and pimagedine with serine protease.
Authors: Ahmad, M.S. / Kalam, N. / Akbar, Z. / Shah, N. / Rasheed, S. / Choudhary, M.I.
History
DepositionApr 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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

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Assembly

Deposited unit
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8355
Polymers23,3241
Non-polymers5114
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.449, 54.449, 106.284
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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, 151 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#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.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-FO9 / famotidine


Mass: 339.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17N7O2S3 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antagonist*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 1.95 Å3/Da / Density % sol: 36.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1-0.4 M Li2SO4, 16% PEG-3350 and 0.1 M HEPES at pH of 7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5406 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Nov 9, 2022
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.1→19.64 Å / Num. obs: 11143 / % possible obs: 99.9 % / Redundancy: 1.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.032 / Net I/σ(I): 20.6
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 0.096 / Mean I/σ(I) obs: 7.7 / Num. unique obs: 892 / CC1/2: 0.89

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PROTEUM PLUSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CE5

1ce5


Resolution: 2.1→19.64 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.879 / SU B: 6.227 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.28 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25087 538 4.8 %RANDOM
Rwork0.17953 ---
obs0.18313 10604 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.771 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-0.21 Å20 Å2
2---0.42 Å20 Å2
3---1.38 Å2
Refinement stepCycle: 1 / Resolution: 2.1→19.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 23 147 1799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131684
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151562
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.6272279
X-RAY DIFFRACTIONr_angle_other_deg1.2911.5833611
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.785218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.21425.08261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30815270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.43152
X-RAY DIFFRACTIONr_chiral_restr0.0610.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021925
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02363
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_it0.8651.385887
X-RAY DIFFRACTIONr_mcbond_other0.8641.384886
X-RAY DIFFRACTIONr_mcangle_it1.4592.0711097
X-RAY DIFFRACTIONr_mcangle_other1.4582.0711098
X-RAY DIFFRACTIONr_scbond_it1.1521.526797
X-RAY DIFFRACTIONr_scbond_other1.1541.515794
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9132.1991176
X-RAY DIFFRACTIONr_long_range_B_refined4.75717.2032029
X-RAY DIFFRACTIONr_long_range_B_other4.70417.1942008
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 24 -
Rwork0.22 774 -
obs--100 %

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