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- PDB-1jim: STEREOSPECIFIC REACTION OF 3-METHOXY-4-CHLORO-7-AMINOISOCOUMARIN ... -

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Basic information

Entry
Database: PDB / ID: 1jim
TitleSTEREOSPECIFIC REACTION OF 3-METHOXY-4-CHLORO-7-AMINOISOCOUMARIN WITH CRYSTALLINE PORCINE PANCREATIC ELASTASE
ComponentsPORCINE PANCREATIC ELASTASE
KeywordsHYDROLASE(SERINE PROTEINASE)
Function / homology
Function and homology information


pancreatic elastase / 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / 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
Chem-ICU / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa domestica (domestic pig)
MethodX-RAY DIFFRACTION / Resolution: 2.31 Å
AuthorsMeyer, E.
Citation
Journal: J.Am.Chem.Soc. / Year: 1985
Title: Stereospecific Reaction of 3-Methoxy-4-Chloro-7-Aminoisocoumarin with Crystalline Porcine Pancreatic Elastase
Authors: Meyer Junior, E.F. / Presta, L.G. / Radhakrishnan, R.
#1: Journal: J.Am.Chem.Soc. / Year: 1992
Title: Design, Synthesis, and Kinetic Evaluation of a Unique Class of Elastase Inhibitors, the Peptidyl Alpha-Ketobenzoxazoles, and the X-Ray Crystal Structure of the Covalent Complex between Porcine ...Title: Design, Synthesis, and Kinetic Evaluation of a Unique Class of Elastase Inhibitors, the Peptidyl Alpha-Ketobenzoxazoles, and the X-Ray Crystal Structure of the Covalent Complex between Porcine Pancreatic Elastase and Ac-Ala-Pro-Val-2-Benzoxazole
Authors: Edwards, P.D. / Meyer Junior, E.F. / Vijayalakshmi, J. / Tuthill, P.A. / Andisik, D.A. / Gomes, B. / Strimpler, A.
History
DepositionMar 19, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _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: PORCINE PANCREATIC ELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2913
Polymers25,9281
Non-polymers3632
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.400, 58.100, 75.200
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 PORCINE PANCREATIC ELASTASE


Mass: 25928.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa domestica (domestic pig) / Species: Sus scrofa / Strain: domestica / References: UniProt: P00772, pancreatic elastase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ICU / METHYL(2-ACETOXY-2-(2-CARBOXY-4-AMINO-PHENYL))ACETATE


Mass: 267.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H13NO6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: EL1_PIG SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE ASP 91 ASN 77

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.18 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 15614 / % possible obs: 70 % / Num. measured all: 42053 / Rmerge(I) obs: 0.071

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Processing

SoftwareName: EREF / Classification: refinement
RefinementRfactor Rwork: 0.153 / Highest resolution: 2.31 Å
Refinement stepCycle: LAST / Highest resolution: 2.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 23 133 1978
Software
*PLUS
Name: EREF / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.31 Å / Rfactor obs: 0.153
Solvent computation
*PLUS
Displacement parameters
*PLUS

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