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Basic information

Entry
Database: PDB / ID: 5est
TitleCrystallographic analysis of the inhibition of porcine pancreatic elastase by a peptidyl boronic acid: structure of a reaction intermediate
ComponentsELASTASE
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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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~2~-[(benzyloxy)carbonyl]-N-[(1R,2S)-1-(dihydroxyboranyl)-2-methylbutyl]-L-alaninamide / Chem-0P2 / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.09 Å
AuthorsTakahashi, L.H. / Radhakrishnan, R. / Rosenfieldjunior, R.E. / Meyerjunior, E.F.
Citation
Journal: Biochemistry / Year: 1989
Title: Crystallographic analysis of the inhibition of porcine pancreatic elastase by a peptidyl boronic acid: structure of a reaction intermediate.
Authors: Takahashi, L.H. / Radhakrishnan, R. / Rosenfield Jr., R.E. / Meyer Jr., E.F.
#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, 1989Processing site: BNL
Revision 1.0Apr 15, 1992Provider: 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 1.3Dec 12, 2012Group: Other
Revision 1.4Jun 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_conn_type / 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 / _struct_conn.conn_type_id / _struct_conn.id / _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_conn_type.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 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4004
Polymers25,9281
Non-polymers4723
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.280, 57.560, 75.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: THE BORON ATOM OF THE INHIBITOR (RESIDUE B2I I 3) IS COVALENTLY BONDED TO THE ACTIVE SITE SER E 195 OG AS WELL AS TO HIS E 57 NE1 WHICH IS DESCRIBED AS A COORDINATE COVALENT BOND.

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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: Chemical ChemComp-0P2 / N~2~-[(benzyloxy)carbonyl]-N-[(1R,2S)-1-(dihydroxyboranyl)-2-methylbutyl]-L-alaninamide / ZAIB


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 336.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25BN2O5 / Details: REACTION INTERMEDIATE
References: N~2~-[(benzyloxy)carbonyl]-N-[(1R,2S)-1-(dihydroxyboranyl)-2-methylbutyl]-L-alaninamide
#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.: 202 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE RESIDUE NUMBERING SCHEME USED FOR ELASTASE WAS CHOSEN TO MAXIMIZE HOMOLOGY WITH THE NUMBERING ...THE RESIDUE NUMBERING SCHEME USED FOR ELASTASE WAS CHOSEN TO MAXIMIZE HOMOLOGY WITH THE NUMBERING FOR CHYMOTRYPSINOGEN A.

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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: 43.08 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.4 %(w/v)PPE solution1drop
20.1 Msodium phosphate1reservoir
30.1 Msodium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Num. all: 19661 / Num. obs: 11021 / Num. measured all: 10569 / Rmerge(I) obs: 0.039

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Processing

SoftwareName: EREF / Classification: refinement
RefinementResolution: 2.09→7 Å / Rfactor Rwork: 0.15
Refinement stepCycle: LAST / Resolution: 2.09→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 29 202 2053
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.017
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_deg2.4
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: 2.2 Å / Rfactor all: 0.148
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: o_angle_d / Dev ideal: 2.4

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