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- PDB-1p01: Serine protease mechanism. structure of an inhibitory complex oF ... -

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Basic information

Entry
Database: PDB / ID: 1p01
TitleSerine protease mechanism. structure of an inhibitory complex oF ALPHA-LYTIC Protease and a tightly bound peptide boronic acid
ComponentsALPHA-LYTIC PROTEASE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


alpha-lytic endopeptidase / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Alpha-lytic protease prodomain / Streptogrisin prodomain / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Alpha-lytic protease prodomain / Streptogrisin prodomain / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / 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-(tert-butoxycarbonyl)-L-alanyl-N-[(1R)-1-(dihydroxyboranyl)-2-methylpropyl]-L-prolinamide / Chem-0EG / Alpha-lytic protease
Similarity search - Component
Biological speciesLysobacter enzymogenes (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsBone, R. / Agard, D.A.
Citation
Journal: Biochemistry / Year: 1987
Title: Serine protease mechanism: structure of an inhibitory complex of alpha-lytic protease and a tightly bound peptide boronic acid.
Authors: Bone, R. / Shenvi, A.B. / Kettner, C.A. / Agard, D.A.
#1: Journal: To be Published
Title: Structure Analysis of Specificity. Alpha-Lytic Protease Complexes with Analogs of Reaction Intermediates
Authors: Bone, R. / Frank, D. / Kettner, C. / Agard, D.A.
#2: Journal: To be Published
Title: Structural Plasticity as a Determinant of Enzyme Specificity. Creating Broadly Specific Proteases
Authors: Bone, R. / Silen, J.L. / Agard, D.A.
#3: Journal: Biochemistry / Year: 1988
Title: Kinetic Properties of the Binding of Alpha-Lytic Protease to Peptide Boronic Acids
Authors: Kettner, C.A. / Bone, R. / Agard, D.A. / Bachovchin, W.W.
#4: Journal: J.Mol.Biol. / Year: 1985
Title: Refined Structure of Alpha-Lytic Protease at 1.7 Angstroms Resolution. Analysis of Hydrogen Bonding and Solvent Structure
Authors: Fujinaga, M. / Delbaere, L.T.J. / Brayer, G.D. / James, M.N.G.
#5: Journal: J.Mol.Biol. / Year: 1979
Title: Molecular Structure of the Alpha-Lytic Protease from Myxobacter 495 at 2.8 Angstroms Resolution
Authors: Brayer, G.D. / Delbaere, L.T.J. / James, M.N.G.
History
DepositionApr 24, 1989Processing site: BNL
Revision 1.0Apr 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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_sheet / 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.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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALPHA-LYTIC PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3563
Polymers19,8751
Non-polymers4812
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.340, 66.340, 80.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: RESIDUE 99A IS A CIS PROLINE.

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Components

#1: Protein ALPHA-LYTIC PROTEASE


Mass: 19875.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lysobacter enzymogenes (bacteria) / Gene: alpha-LP / References: UniProt: P00778, alpha-lytic endopeptidase
#2: Chemical ChemComp-0EG / N-(tert-butoxycarbonyl)-L-alanyl-N-[(1R)-1-(dihydroxyboranyl)-2-methylpropyl]-L-prolinamide / N-tert-butyloxycarbonylalanylprolylvaline boronic acid


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 385.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H32BN3O6
References: N-(tert-butoxycarbonyl)-L-alanyl-N-[(1R)-1-(dihydroxyboranyl)-2-methylpropyl]-L-prolinamide
#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.: 141 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsINHIBITORY PEPTIDE BORONIC ACIDS ARE PEPTIDE ANALOGUES IN WHICH THE C-TERMINAL CARBOXY GROUP (COOH) ...INHIBITORY PEPTIDE BORONIC ACIDS ARE PEPTIDE ANALOGUES IN WHICH THE C-TERMINAL CARBOXY GROUP (COOH) HAS BEEN REPLACED WITH THE BORONIC ACID GROUP (B(OH)2).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal grow
*PLUS
Method: microdialysis / Details: Brayer, G.D., (1979) J.Mol.Biol., 131, 743.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.8 M11Li2SO4
210 mg/mlprotein12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.138 / Highest resolution: 2 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1391 0 32 141 1564
Refine LS restraints
*PLUS
Type: p_bond_d / Dev ideal: 0.018

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