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- PDB-1elb: Analogous inhibitors of elastase do not always bind analogously -

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Basic information

Entry
Database: PDB / ID: 1elb
TitleAnalogous inhibitors of elastase do not always bind analogously
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 / 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
TRIFLUOROACETYL-L-LYSYL-L-LEUCYL-P-ISOPROPYLANILIDE / Chem-0Z4 / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsMattos, C. / Rasmussen, B. / Ding, X. / Petsko, G.A. / Ringe, D.
Citation
Journal: Nat.Struct.Biol. / Year: 1994
Title: Analogous inhibitors of elastase do not always bind analogously.
Authors: Mattos, C. / Rasmussen, B. / Ding, X. / Petsko, G.A. / Ringe, D.
#1: Journal: J.Mol.Recog. / Year: 1990
Title: Interaction of the Peptide Cf3-Leu-Ala-Nh-C6H4-Cf3 (Tfla) with Porcine Pancreatic Elastase. X-Ray Studies at 1.8 Angstroms
Authors: Li De La Sierra, I. / Papamichael, E. / Sakarelos, C. / Dimicoli, J.-L. / Prange, T.
#2: 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.
#3: Journal: J.Mol.Biol. / Year: 1986
Title: Structure of the Product Complex of Acetyl-Ala-Pro-Ala with Porcine Pancreatic Elastase at 1.65 Angstroms Resolution
Authors: Meyer, E. / Radhakrishnan, R. / Cole, G. / Presta, L.G.
#4: Journal: J.Mol.Biol. / Year: 1982
Title: Crystallographic Study of the Binding of a Tri-Fluoroacetyl Dipeptide Anilide Inhibitor with Elastase
Authors: Hughes, D.L. / Diecker, L.C. / Bieth, L.C. / Dimicoli, J.-L.
#5: 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.
#6: 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
DepositionDec 7, 1993Processing site: BNL
Revision 1.0Jun 22, 1994Provider: 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 / 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 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification
Remark 700SHEET THE SHEETS PRESENTED AS *S1* AND *S2* IN SHEET RECORDS BELOW ARE ACTUALLY TWO SIX-STRANDED ...SHEET THE SHEETS PRESENTED AS *S1* AND *S2* IN SHEET RECORDS BELOW ARE ACTUALLY TWO SIX-STRANDED BETA BARRELS. THIS IS REPRESENTED BY TWO SEVEN-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS OF EACH SHEET ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5384
Polymers25,9281
Non-polymers6103
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.690, 58.050, 75.250
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 genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00772, pancreatic elastase
#2: Chemical ChemComp-0Z4 / 6-ammonio-N-(trifluoroacetyl)-L-norleucyl-N-[4-(1-methylethyl)phenyl]-L-leucinamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 473.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H36F3N4O3
References: TRIFLUOROACETYL-L-LYSYL-L-LEUCYL-P-ISOPROPYLANILIDE
#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.: 126 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE IDENTITY OF ASN A 81 AGREES WITH THE SEQUENCES OF SEVERAL OTHER ELASTASE STRUCTURES. THE ...THE IDENTITY OF ASN A 81 AGREES WITH THE SEQUENCES OF SEVERAL OTHER ELASTASE STRUCTURES. THE AUTHORS, THEREFORE, BELIEVE IT TO BE CORRECT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growDetails: THE COMPLEX WAS DONE BY SOAKING OF THE INHIBITOR. THE NATIVE ELASTASE CRYSTALS WERE TRANSFERRED FROM THE SITTING DROP TO A HIGH-SALT MOTHER LIQUOR CONTAINING THE TFA-LYS-PRO-ISO INHIBITOR AT ...Details: THE COMPLEX WAS DONE BY SOAKING OF THE INHIBITOR. THE NATIVE ELASTASE CRYSTALS WERE TRANSFERRED FROM THE SITTING DROP TO A HIGH-SALT MOTHER LIQUOR CONTAINING THE TFA-LYS-PRO-ISO INHIBITOR AT A CONCENTRATION OF 0.1 MILLIMOLAR. THE INHIBITOR WAS SOAKED FOR FOUR DAYS.
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
170 %methanol1reservoir
230 %acetate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.06 Å

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→10 Å / Rfactor Rwork: 0.15 / Rfactor obs: 0.15 / σ(F): 0
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 39 126 1987
Refinement
*PLUS
Rfactor all: 0.15 / Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS

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