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- PDB-2v35: Porcine Pancreatic Elastase in complex with inhibitor JM54 -

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Basic information

Entry
Database: PDB / ID: 2v35
TitlePorcine Pancreatic Elastase in complex with inhibitor JM54
ComponentsELASTASE-1
KeywordsHYDROLASE / SERINE PROTEASE / SERINE PROTEASES / CALCIUM / ZYMOGEN / PROTEASE / ELASTASE / INHIBITION / BETA-LACTAMS / METAL-BINDING
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
Chem-J54 / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsOliveira, T.F. / Mulchande, J. / Martins, L. / Moreira, R. / Iley, J. / Archer, M.
Citation
Journal: Org.Biomol.Chem. / Year: 2007
Title: The Efficiency of C-4 Substituents in Activating the Beta-Lactam Scaffold Towards Serine Proteases and Hydroxide Ion.
Authors: Mulchande, J. / Martins, L. / Moreira, R. / Archer, M. / Oliveira, T.F. / Iley, J.
#1: Journal: Protein Pept.Lett. / Year: 2007
Title: Crystallization and Preliminary Diffraction Studies of Porcine Pancreatic Elastase in Complex with a Novel Inhibitor
Authors: Oliveira, T.F. / Mulchande, J. / Moreira, R. / Iley, J. / Archer, M.
History
DepositionJun 12, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.pdbx_dist_value / _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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ELASTASE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4706
Polymers25,9291
Non-polymers5415
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.246, 57.938, 74.688
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ELASTASE-1 / PORCINE PANCREATIC ELASTASE


Mass: 25929.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: PANCREAS / References: UniProt: P00772, pancreatic elastase

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Non-polymers , 5 types, 315 molecules

#2: Chemical ChemComp-J54 / (2R)-3-{[(BENZYLAMINO)CARBONYL]AMINO}-2-HYDROXYPROPANOIC ACID


Mass: 238.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14N2O4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHIS SEQUENCE BELONGS TO THE PRECURSOR OF PORCINE PANCREATIC ELASTASE. FOR THE CRYSTALLOGRAPHIC ...THIS SEQUENCE BELONGS TO THE PRECURSOR OF PORCINE PANCREATIC ELASTASE. FOR THE CRYSTALLOGRAPHIC STUDIES HAVE BEEN USED THE AMINO-ACID SEQUENCE FROM 27 TO 266

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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: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growpH: 5.1 / Details: 100 MM SODIUM ACETATE PH 5.1 200 MM SODIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.82
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 2, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82 Å / Relative weight: 1
ReflectionResolution: 1.66→37.9 Å / Num. obs: 26474 / % possible obs: 96.9 % / Observed criterion σ(I): 6 / Redundancy: 4.3 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 27.4
Reflection shellResolution: 1.66→1.75 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 14.7 / % possible all: 79.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QNJ

1qnj


Resolution: 1.67→33.84 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.487 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.186 1310 5.1 %RANDOM
Rwork0.156 ---
obs0.158 24355 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.67→33.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 34 310 2166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211906
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.221.9282599
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8615238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69123.92984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.44715281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1961512
X-RAY DIFFRACTIONr_chiral_restr0.090.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021450
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.2913
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21294
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.4780.2244
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.225
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6341.51181
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.17321906
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8753771
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9294.5693
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.67→1.71 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.284 74
Rwork0.208 1469

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