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- PDB-1btu: PORCINE PANCREATIC ELASTASE COMPLEXED WITH (3S, 4R)-1-TOLUENESULP... -

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Basic information

Entry
Database: PDB / ID: 1btu
TitlePORCINE PANCREATIC ELASTASE COMPLEXED WITH (3S, 4R)-1-TOLUENESULPHONYL-3-ETHYL-AZETIDIN-2-ONE-4-CARBOXYLIC ACID
ComponentsELASTASE
KeywordsSERINE PROTEASE / HYDROLASE / 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
Chem-2BL / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY REFINEMENT / Resolution: 1.6 Å
AuthorsWilmouth, R.C. / Clifton, I.J. / Schofield, C.J.
Citation
Journal: Biochemistry / Year: 1998
Title: Inhibition of elastase by N-sulfonylaryl beta-lactams: anatomy of a stable acyl-enzyme complex.
Authors: Wilmouth, R.C. / Westwood, N.J. / Anderson, K. / Brownlee, W. / Claridge, T.D. / Clifton, I.J. / Pritchard, G.J. / Aplin, R.T. / Schofield, C.J.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Structure of a Specific Acyl-Enzyme Complex Formed between Beta-Casomorphin-7 and Porcine Pancreatic Elastase
Authors: Wilmouth, R.C. / Clifton, I.J. / Robinson, C.V. / Roach, P.L. / Aplin, R.T. / Westwood, N.J. / Hajdu, J. / Schofield, C.J.
#2: Journal: Arch.Biochem.Biophys. / Year: 1992
Title: Inhibition of Human Serine Proteases by Substituted 2-Azetidinones
Authors: Knight, W.B. / Chabin, R. / Green, B.
#3: Journal: Biochemistry / Year: 1992
Title: Specificity, Stability, and Potency of Monocyclic Beta-Lactam Inhibitors of Human Leucocyte Elastase
Authors: Knight, W.B. / Green, B.G. / Chabin, R.M. / Gale, P. / Maycock, A.L. / Weston, H. / Kuo, D.W. / Westler, W.M. / Dorn, C.P. / Finke, P.E. / Hagmann, W.K. / Hale, J.J. / Liesch, J. / Maccoss, ...Authors: Knight, W.B. / Green, B.G. / Chabin, R.M. / Gale, P. / Maycock, A.L. / Weston, H. / Kuo, D.W. / Westler, W.M. / Dorn, C.P. / Finke, P.E. / Hagmann, W.K. / Hale, J.J. / Liesch, J. / Maccoss, M. / Navia, M.A. / Shah, S.K. / Underwood, D. / Doherty, J.B.
#4: Journal: Tetrahedron / Year: 1990
Title: Monocyclic Beta-Lactam Inhibitors of Human Leukocyte Elastase
Authors: Firestone, R.A. / Barker, P.L. / Pisano, J.M. / Ashe, B.M. / Dahlgren, M.E.
#5: Journal: Acta Crystallogr.,Sect.B / Year: 1988
Title: Structure of Native Porcine Pancreatic Elastase at 1.65 A Resolution
Authors: Meyer, E. / Cole, G. / Radhakrishnan, R. / Epp, O.
History
DepositionSep 1, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_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

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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)26,3804
Polymers25,9281
Non-polymers4513
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.570, 57.930, 74.720
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 / PPE


Mass: 25928.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PORCINE PANCREATIC ELASTASE / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00772, pancreatic elastase
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-2BL / (3R)-3-ethyl-N-[(4-methylphenyl)sulfonyl]-L-aspartic acid


Mass: 315.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17NO6S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 33.2 %
Crystal growpH: 5 / Details: pH 5.0
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 %(w/v)protein11
20.1 Msodium acetate11
30.02 %(w/v)sodium azide11
40.1 Msodium sulphate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.6→23.8 Å / Num. obs: 29200 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 5.67 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 17.4
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 8.4 / % possible all: 95.5
Reflection
*PLUS
Num. measured all: 165584
Reflection shell
*PLUS
% possible obs: 95.5 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97model building
X-PLORmodel building
SHELXL-97refinement
X-PLORrefinement
SHELXL-97phasing
X-PLORphasing
RefinementMethod to determine structure: RIGID BODY REFINEMENT / Resolution: 1.6→23.8 Å / Num. parameters: 8219 / Num. restraintsaints: 7616 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: REFMAC ALSO USED
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1168 4 %RANDOM
all0.192 29200 --
obs0.192 -98.7 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2054
Refinement stepCycle: LAST / Resolution: 1.6→23.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 26 206 2054
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.025
X-RAY DIFFRACTIONs_zero_chiral_vol0.059
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.074
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.006
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.036
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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