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- PDB-2est: Crystallographic study of the binding of a trifluoroacetyl dipept... -

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Basic information

Entry
Database: PDB / ID: 2est
TitleCrystallographic study of the binding of a trifluoroacetyl dipeptide anilide inhibitor with elastase
ComponentsELASTASE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / 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
Trifluoroacetyl dipeptide anilide inhibitor, TFA LYS ALA ANI / Chem-2Z5 / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsSieker, L.C. / Hughes, D.L.
Citation
Journal: J.Mol.Biol. / Year: 1982
Title: Crystallographic study of the binding of a trifluoroacetyl dipeptide anilide inhibitor with elastase.
Authors: Hughes, D.L. / Sieker, L.C. / Bieth, J. / Dimicoli, J.L.
#1: Journal: Eur.J.Biochem. / Year: 1980
Title: The Indirect Mechanism of Action of the Trifluoroacetyl Peptides on Elastase
Authors: Dimicoli, J.-L. / Renaud, A. / Bieth, J.
#2: Journal: J.Mol.Biol. / Year: 1978
Title: The Atomic Structure of Crystalline Porcine Pancreatic Elastase at 2.5 Angstroms Resolution. Comparisons with the Structure of Alpha-Chymotrypsin
Authors: Sawyer, L. / Shotton, C.M. / Campbell, J.W. / Wendell, P.L. / Muirhead, H. / Watson, H.C. / Diamond, R. / Ladner, R.C.
History
DepositionMar 24, 1986Processing site: BNL
Revision 1.0May 7, 1986Provider: 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 1.4Feb 14, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THE TWO SEVEN STRANDED SHEETS IN THIS STRUCTURE ARE REALLY SIX STRANDED BETA BARRELS - THIS ...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

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Assembly

Deposited unit
E: ELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4813
Polymers25,9281
Non-polymers5532
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.530, 57.470, 75.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: SEE REMARK 7.

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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) / Organ: PANCREAS / References: UniProt: P00772, pancreatic elastase
#2: Chemical ChemComp-2Z5 / 6-ammonio-N-(trifluoroacetyl)-L-norleucyl-N-[4-(trifluoromethyl)phenyl]-L-alaninamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 457.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H23F6N4O3
References: Trifluoroacetyl dipeptide anilide inhibitor, TFA LYS ALA ANI
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUE NUMBERING IS BASED ON THAT OF CHYMOTRYPSINOGEN A. THE ENZYME HAS BEEN ASSIGNED CHAIN ...THE RESIDUE NUMBERING IS BASED ON THAT OF CHYMOTRYPSINOGEN A. THE ENZYME HAS BEEN ASSIGNED CHAIN IDENTIFIER *E*

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5 / Method: unknown / Details: Shotton, D.M., (1968) J.Mol.Biol., 32, 155.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 %solution of elastase11
20.01 Msodium acetate11
30.02 Msodium sulfate11

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Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 8481 / Num. measured all: 15401

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.21 / Highest resolution: 2.5 Å
Details: NOTE THAT THE SG - SG DISTANCES FOR THE FOUR DISULFIDE BRIDGES ARE ALL ABOUT 3 ANGSTROMS.
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 32 45 1899
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.04
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg4
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Num. reflection obs: 7187 / σ(I): 2 / Rfactor obs: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15.7 Å2
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 4

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