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- PDB-1nes: STRUCTURE OF THE PRODUCT COMPLEX OF ACETYL-ALA-PRO-ALA WITH PORCI... -

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Entry
Database: PDB / ID: 1nes
TitleSTRUCTURE OF THE PRODUCT COMPLEX OF ACETYL-ALA-PRO-ALA WITH PORCINE PANCREATIC ELASTASE AT 1.65 ANGSTROMS RESOLUTION
Components
  • ACETYL-ALA-PRO-ALA
  • ELASTASE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE/INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
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
Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 1.65 Å
AuthorsMeyer Junior, E.F. / Radhakrishnan, R. / M Cole, G. / Presta, L.G.
Citation
Journal: J.Mol.Biol. / Year: 1986
Title: Structure of the product complex of acetyl-Ala-Pro-Ala with porcine pancreatic elastase at 1.65 A resolution.
Authors: Meyer Jr., E.F. / Radhakrishnan, R. / Cole, G.M. / Presta, L.G.
#1: Journal: To be Published
Title: Misbehaving Macromolecules: Backwards Binding Ligands and Other Surprising Structures
Authors: Meyer, E.F. / Botos, I. / Scapozza, L. / Zhang, D.
#2: 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. / Meyer Junior, E.F.
#3: Journal: Biochemistry / Year: 1991
Title: Complexed with 7-Amino-3-(2-Bromoethoxy)-4-Chloroisocoumarin as a Nonreactivatable Doubly Covalent Enzyme-Inhibitor Complex
Authors: Vijayalakshmi, J. / Meyer Junior, E.F. / Kam, C.-M. / Powers, J.C.
#4: 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. / Meyer Junior, E.F.
#5: 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. / Meyer Junior, E.F. / Bode, W. / Kam, C.-M. / Radhakrishnan, R. / Vijayalakshmi, J. / Powers, J.C.
#6: 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. / Meyer Junior, E.F. / Powers, J.C.
#7: Journal: Acta Crystallogr.,Sect.B / Year: 1988
Title: Structure of Native Porcine Pancreatic Elastase at 1.65 Angstroms Resolution
Authors: Meyer, E. / Cole, G. / Radhakrishnan, R. / Epp, O.
#8: 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. / Meyer Junior, E.F. / Wildonger, R.
#9: 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. / Meyer Junior, E.F. / Wildonger, R.
#10: Journal: J.Am.Chem.Soc. / Year: 1985
Title: Stereospecific Reaction of 3-Methoxy-4-Chloro-7-Amino-Isocoumarin with Crystalline Porcine Pancreatic Elastase
Authors: Meyer Junior, E.F. / Presta, L.G. / Radhakrishnan, R.
History
DepositionJul 31, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 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_asym_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_asym_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 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: ELASTASE
I: ACETYL-ALA-PRO-ALA
J: ACETYL-ALA-PRO-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6315
Polymers26,4953
Non-polymers1362
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-30 kcal/mol
Surface area10340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.400, 58.200, 75.400
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 ELASTASE


Mass: 25928.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00772, pancreatic elastase
#2: Protein/peptide ACETYL-ALA-PRO-ALA


Mass: 283.323 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.13 Å3/Da / Density % sol: 42.19 %
Crystal grow
*PLUS
pH: 5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 %(w/v)PPEase11
20.1 Msodium acetate11
30.02 %(w/v)sodium azide11
40.1 Msodium sulphate12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionObserved criterion σ(F): 2
Reflection
*PLUS
Highest resolution: 1.65 Å / Num. obs: 20665 / % possible obs: 72 %

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Processing

SoftwareName: EREF / Classification: refinement
RefinementResolution: 1.65→7 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.184 --
obs-20310 72 %
Refinement stepCycle: LAST / Resolution: 1.65→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1854 0 6 138 1998
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONo_bond_d
X-RAY DIFFRACTIONo_angle_deg

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