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- PDB-1smf: Studies on an artificial trypsin inhibitor peptide derived from t... -

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Basic information

Entry
Database: PDB / ID: 1smf
TitleStudies on an artificial trypsin inhibitor peptide derived from the mung bean inhibitor
Components
  • BOWMAN-BIRK TYPE TRYPSIN INHIBITOR
  • TRYPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Bowman-Birk serine protease inhibitor family / Bowman-Birk serine protease inhibitors family signature. / Proteinase inhibitor I12, Bowman-Birk / Bowman-Birk type proteinase inhibitor / Bowman-Birk type proteinase inhibitor / : / 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 ...Bowman-Birk serine protease inhibitor family / Bowman-Birk serine protease inhibitors family signature. / Proteinase inhibitor I12, Bowman-Birk / Bowman-Birk type proteinase inhibitor / Bowman-Birk type proteinase inhibitor / : / 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
Serine protease 1 / Bowman-Birk type trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsHuang, Q. / Li, Y. / Zhang, S. / Liu, S. / Tang, Y. / Qi, C.
CitationJournal: J.Biochem.(Tokyo) / Year: 1994
Title: Studies on an artificial trypsin inhibitor peptide derived from the mung bean trypsin inhibitor: chemical synthesis, refolding, and crystallographic analysis of its complex with trypsin.
Authors: Li, Y. / Huang, Q. / Zhang, S. / Liu, S. / Chi, C. / Tang, Y.
History
DepositionOct 24, 1992Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Jun 28, 2017Group: Database references / Other
Category: pdbx_database_status / struct_ref / struct_ref_seq
Item: _pdbx_database_status.process_site
Revision 1.4Oct 9, 2024Group: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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
E: TRYPSIN
I: BOWMAN-BIRK TYPE TRYPSIN INHIBITOR
E: CALCIUM ION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7773
Polymers25,7372
Non-polymers401
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-17 kcal/mol
Surface area9210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.230, 63.620, 69.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO I 14

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Components

#1: Protein TRYPSIN


Mass: 23324.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Tissue: PANCREAS / References: UniProt: P00760, trypsin
#2: Protein/peptide BOWMAN-BIRK TYPE TRYPSIN INHIBITOR


Mass: 2412.808 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: P01062
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsBOWMAN-BIRK INHIBITOR IS A SYNTHESIZED PEPTIDE BASED ON MIMIC MUNG BEAN TRYPSIN INHIBITOR LYSINE ...BOWMAN-BIRK INHIBITOR IS A SYNTHESIZED PEPTIDE BASED ON MIMIC MUNG BEAN TRYPSIN INHIBITOR LYSINE FRAGMENT. THE SEQUENCE GIVEN BELOW IS THE CORRECTED SEQUENCE OF LI, Y. L. CHI, C. W. (SCIENCE IN CHINA, B24, 42, 1994). THE SEQUENCE DIFFERS FROM THAT OF SWISS-PROT ENTRY IBB_PHAAU AT THE FOLLOWING POSITIONS: SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ LYS 22 ILE I 13 GLN 25 GLU I 16

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal grow
*PLUS
Temperature: 24 ℃ / pH: 6.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 Mammonium sulfate1drop
20.2 Mphosphate1drop
32 Mammonium sulfate1reservoir
40.2 Mphosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 12563 / % possible obs: 82.8 % / Num. measured all: 42768 / Rmerge(I) obs: 0.0768

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.19 / Rfactor obs: 0.19 / Highest resolution: 2.1 Å
Refinement stepCycle: LAST / Highest resolution: 2.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1694 0 1 83 1778
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.71
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d15.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.193 / Rfactor Rwork: 0.193 / Highest resolution: 2.2 Å / Lowest resolution: 7 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d2.71
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg

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