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- PDB-4est: CRYSTAL STRUCTURE OF THE COVALENT COMPLEX FORMED BY A PEPTIDYL AL... -

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Basic information

Entry
Database: PDB / ID: 4est
TitleCRYSTAL STRUCTURE OF THE COVALENT COMPLEX FORMED BY A PEPTIDYL ALPHA,ALPHA-DIFLUORO-BETA-KETO AMIDE WITH PORCINE PANCREATIC ELASTASE AT 1.78-ANGSTROMS RESOLUTION
Components
  • ELASTASE
  • INHIBITOR ACE-ALA-PRO-VAI-DIFLUORO-N-PHENYLETHYLACETAMIDE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEINASE / 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
N-acetyl-L-alanyl-N-{(1S)-3,3-difluoro-1-(1-methylethyl)-2,4-dioxo-4-[(2-phenylethyl)amino]butyl}-L-prolinamide / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 1.78 Å
AuthorsTakahashi, L.H. / Radhakrishnan, R. / Rosenfieldjunior, R.E. / Meyerjunior, E.F. / Trainor, D.A.
Citation
Journal: J.Am.Chem.Soc. / Year: 1989
Title: Crystal Structure of the Covalent Complex Formed by a Peptidyl Alpha,Alpha-Difluoro-Beta-Keto Amide with Porcine Pancreatic Elastase at 1.78-Angstroms Resolution
Authors: Takahashi, L.H. / Radhakrishnan, R. / Rosenfieldjunior, R.E. / Meyerjunior, E.F. / Trainor, D.A.
#1: 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.
History
DepositionMay 15, 1989Deposition site: BNL / Processing site: BNL
Revision 1.0Apr 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 10, 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 1.3Dec 12, 2012Group: Other
Revision 1.4Sep 18, 2013Group: Structure summary
Revision 2.0Oct 3, 2018Group: Data collection / Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 3.0Jul 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / 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 / _entity_poly.pdbx_seq_one_letter_code_can / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 3.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700SHEET THE TWO SEVEN STRANDED SHEETS IN THIS STRUCTURE ARE REALLY SIX STRANDED BETA BARRELS. THIS IS ...SHEET THE TWO SEVEN STRANDED SHEETS IN THIS STRUCTURE ARE REALLY SIX STRANDED BETA BARRELS. THIS IS DENOTED BY THE FIRST STRAND RECURRING AS THE LAST STRAND.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: ELASTASE
I: INHIBITOR ACE-ALA-PRO-VAI-DIFLUORO-N-PHENYLETHYLACETAMIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6394
Polymers26,5032
Non-polymers1362
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.240, 58.170, 75.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: ATOM OG OF SER E 195 OF THE ENZYME IS COVALENTLY BONDED TO THE CARBONYL CARBON ATOM OF VAI I 4 OF THE INHIBITOR.

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Components

#1: Protein ELASTASE


Mass: 25928.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Tissue: PANCREAS / References: UniProt: P00772, pancreatic elastase
#2: Protein/peptide INHIBITOR ACE-ALA-PRO-VAI-DIFLUORO-N-PHENYLETHYLACETAMIDE


Type: Peptide-like / Class: Inhibitor / Mass: 574.479 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: N-acetyl-L-alanyl-N-{(1S)-3,3-difluoro-1-(1-methylethyl)-2,4-dioxo-4-[(2-phenylethyl)amino]butyl}-L-prolinamide
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 156 / 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: 42.25 %
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.78 Å / Num. obs: 16151 / % possible obs: 71 % / Observed criterion σ(I): 1 / Num. measured all: 36367 / Rmerge(I) obs: 0.087

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Processing

SoftwareName: EREF / Classification: refinement
RefinementResolution: 1.78→7 Å / Rfactor Rwork: 0.16
Refinement stepCycle: LAST / Resolution: 1.78→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 6 156 2020
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.012
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.28
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Highest resolution: 1.78 Å / Lowest resolution: 7 Å / Num. reflection obs: 16151
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: o_angle_d / Dev ideal: 2.28

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