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- PDB-9est: STRUCTURAL STUDY OF PORCINE PANCREATIC ELASTASE COMPLEXED WITH 7-... -

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Entry
Database: PDB / ID: 9est
TitleSTRUCTURAL STUDY OF PORCINE PANCREATIC ELASTASE COMPLEXED WITH 7-AMINO-3-(2-BROMOETHOXY)-4-CHLOROISOCOUMARIN AS A NONREACTIVATABLE DOUBLY COVALENT ENZYME-INHIBITOR COMPLEX
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 / 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
(2-BROMOETHYL)(2-'FORMYL-4'-AMINOPHENYL) ACETATE / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsRadhakrishnan, R. / Powers, J.C. / Meyer Jr., E.F.
Citation
Journal: Biochemistry / Year: 1991
Title: Structural study of porcine pancreatic elastase complexed with 7-amino-3-(2-bromoethoxy)-4-chloroisocoumarin as a nonreactivatable doubly covalent enzyme-inhibitor complex.
Authors: Vijayalakshmi, J. / Meyer Jr., E.F. / Kam, C.M. / Powers, J.C.
#1: Journal: J.Med.Chem. / Year: 1992
Title: Effect of the 7-Amino Substituent on the Inhibitory Potency of Mechanism-Based Isocoumarin Inhibitors for Porcine Pancreatic and Human Neutrophil Elastases: A 1.85-Angstroms X-Ray Structure of ...Title: Effect of the 7-Amino Substituent on the Inhibitory Potency of Mechanism-Based Isocoumarin Inhibitors for Porcine Pancreatic and Human Neutrophil Elastases: A 1.85-Angstroms X-Ray Structure of the Complex between Porcine Pancreatic Elastase and 7-[(N-Tosylphenylalanyl)Amino]-4-Chloro-3-Methoxyisocoumarin
Authors: Hernandez, M.A. / Powers, J.C. / Glinski, J. / Oleksyszyn, J. / Vijayalakshmi, J. / Meyerjunior, E.F.
#2: Journal: Biochemistry / Year: 1990
Title: Reaction of Porcine Pancreatic Elastase with 7-Substituted 3-Alkoxy-4-Chloroisocoumarins: Design of Potent Inhibitors Using the Crystal Structure of the Complex Formed with 4-Chloro-3-Ethoxy-7- ...Title: Reaction of Porcine Pancreatic Elastase with 7-Substituted 3-Alkoxy-4-Chloroisocoumarins: Design of Potent Inhibitors Using the Crystal Structure of the Complex Formed with 4-Chloro-3-Ethoxy-7-Guanidino-Isocoumarin
Authors: Powers, J.C. / Oleksyszyn, J. / Narasimhan, S.L. / Kam, C.-M. / Radhakrishnan, R. / Meyerjunior, E.F.
#3: Journal: J.Am.Chem.Soc. / Year: 1990
Title: The 2.2-Angstrom Resolution X-Ray Crystal Structure of the Complex of Trypsin Inhibited by 4-Chloro-3-Ethoxy-7-Guanidinoisocoumarin: A Proposed Model of the Thrombin-Inhibitor Complex
Authors: Chow, M.M. / Meyerjunior, E.F. / Bode, W. / Kam, C.-M. / Radhakrishnan, R. / Vijayalakshmi, J. / Powers, J.C.
#4: Journal: Biochemistry / Year: 1989
Title: Human Leukocyte and Porcine Pancreatic Elastase: X-Ray Crystal Structures, Mechanism, Substrate Specificity, and Mechanism-Based Inhibitors
Authors: Bode, W. / Meyerjunior, E.F. / Powers, J.C.
#5: Journal: J.Mol.Biol. / Year: 1987
Title: Crystal Structures of the Complex of Porcine Pancreatic Elastase with Two Valine-Derived Benzoxazinone Inhibitors
Authors: Radhakrishnan, R. / Presta, L.G. / Meyerjunior, E.F. / Wildonger, R.
#6: Journal: J.Am.Chem.Soc. / Year: 1985
Title: Stereospecific Reaction of 3-Methoxy-4-Chloro-7-Amino-Isocoumarin with Crystalline Porcine Pancreatic Elastase
Authors: Meyerjunior, E.F. / Presta, L.G. / Radhakrishnan, R.
History
DepositionJan 14, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 / pdbx_struct_conn_angle / 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 / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Revision 1.4Oct 9, 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: PORCINE PANCREATIC ELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3504
Polymers25,9281
Non-polymers4223
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.130, 58.140, 75.450
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 (pig) / 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-IBR / (2-BROMOETHYL)(2-'FORMYL-4'-AMINOPHENYL) ACETATE


Mass: 286.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12BrNO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE BOND BETWEEN C1 AND O2 OF 7-*AMINO-3-(2-BROMOETHOXY)-4-CHLOROISOCOUMARIN HAS BEEN BROKEN AND C4 ...THE BOND BETWEEN C1 AND O2 OF 7-*AMINO-3-(2-BROMOETHOXY)-4-CHLOROISOCOUMARIN HAS BEEN BROKEN AND C4 (C2 OF IBR) IS NO LONGER BONDED TO CL BUT TO NE2 OF HIS E 57. IN ADDITION, C' OF IBR IS COVALENTLY BOUND TO OG OF SER 195.
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 ASN 77 ASP 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: 43.11 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.2 %(w/v)PPE11
30.1 Msodium phosphate12
47 %acetonitrile12
27-amino-3-(2-bromoethoxy)-4-chloroisocoumarin11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 6 Å / Num. all: 17673 / Num. obs: 11586 / Observed criterion σ(I): 2
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.94 Å / Num. possible: 35 / Rmerge(I) obs: 0.151

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 1.9→6 Å / σ(F): 2 /
RfactorNum. reflection
obs0.171 11586
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 22 133 1977
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg1.12
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_d / Dev ideal: 1.12

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