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- PDB-5ptp: STRUCTURE OF HYDROLASE (SERINE PROTEINASE) -

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Basic information

Entry
Database: PDB / ID: 5ptp
TitleSTRUCTURE OF HYDROLASE (SERINE PROTEINASE)
ComponentsBETA TRYPSIN
KeywordsSERINE PROTEASE / HYDROLASE / DIGESTION / PANCREAS / ZYMOGEN
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 / 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
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.34 Å
AuthorsStroud, R.M. / Finer-Moore, J.
Citation
Journal: Proteins / Year: 1992
Title: Solvent structure in crystals of trypsin determined by X-ray and neutron diffraction.
Authors: Finer-Moore, J.S. / Kossiakoff, A.A. / Hurley, J.H. / Earnest, T. / Stroud, R.M.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1979
Title: The Accuracy of Refined Protein Structures, Comparison of Two Independently Refined Models of Bovine Trypsin
Authors: Chambers, J.L. / Stroud, R.M.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1977
Title: Difference-Fourier Refinement of the Structure of Dip-Trypsin at 1.5 Angstroms Using a Minicomputer Technique
Authors: Chambers, J.L. / Stroud, R.M.
#3: Journal: PROTEASES AND BIOLOGICAL CONTROL / Year: 1975
Title: Structure-Function Relationships in the Serine Proteases
Authors: Stroud, R.M. / Krieger, M. / Koeppe II, R.E. / Kossiakoff, A.A. / Chambers, J.L.
#4: Journal: Biochem.Biophys.Res.Commun. / Year: 1974
Title: Silver Ion Inhibition of Serine Proteases: Crystallographic Study of Silver-Trypsin
Authors: Chambers, J.L. / Christoph, G.G. / Krieger, M. / Kay, L. / Stroud, R.M.
#5: Journal: J.Mol.Biol. / Year: 1974
Title: The Structure of Bovine Trypsin: Electron Density Maps of the Inhibited Enzyme at 5 a and at 2.7 A Resolution
Authors: Stroud, R.M. / Kay, L.M. / Dickerson, R.E.
#6: Journal: J.Mol.Biol. / Year: 1974
Title: Structure and Specific Binding of Trypsin: Comparison of Inhibited Derivatives and a Model for Substrate Binding
Authors: Krieger, M. / Kay, L.M. / Stroud, R.M.
#7: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1972
Title: The Crystal and Molecular Structure of Dip-Inhibited Bovine Trypsin at 2.7 A Resolution
Authors: Stroud, R.M. / Kay, L.M. / Dickerson, R.E.
#8: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
History
DepositionMar 31, 1997Processing site: BNL
SupersessionJul 7, 1997ID: 4PTP
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4862
Polymers23,4461
Non-polymers401
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.840, 58.610, 67.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BETA TRYPSIN


Mass: 23446.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00760, trypsin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.79 %
Crystal grow
*PLUS
pH: 7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
280 %beta-trypsin11
320 %alpha-trypsin11
1ammonium sulfate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.34→7 Å
Details: THE TRYPSIN IN THE CRYSTAL CONTAINS ABOUT 50 PER-CENT ALPHA-TRYPSIN WHICH IS AUTOLYTICALLY CLEAVED BETWEEN LYS 145 AND SER 146. THE DENSITY IN THE MAP AT THIS POINT IS WEAK BUT APPEARS TO ...Details: THE TRYPSIN IN THE CRYSTAL CONTAINS ABOUT 50 PER-CENT ALPHA-TRYPSIN WHICH IS AUTOLYTICALLY CLEAVED BETWEEN LYS 145 AND SER 146. THE DENSITY IN THE MAP AT THIS POINT IS WEAK BUT APPEARS TO ARISE FROM THE UNCLEAVED COMPONENT.
RfactorNum. reflection
Rwork0.152 -
obs-30041
Displacement parametersBiso mean: 16 Å2
Refinement stepCycle: LAST / Resolution: 1.34→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1648 0 8 211 1867
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d0.052
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.3
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it3.6
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor obs: 0.152
Solvent computation
*PLUS
Displacement parameters
*PLUS

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