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- PDB-1p03: STRUCTURE ANALYSIS OF SPECIFICITY. ALPHA-LYTIC PROTEASE COMPLEXES... -

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Basic information

Entry
Database: PDB / ID: 1p03
TitleSTRUCTURE ANALYSIS OF SPECIFICITY. ALPHA-LYTIC PROTEASE COMPLEXES WITH ANALOGUES OF REACTION INTERMEDIATES
Components
  • ALPHA-LYTIC PROTEASE
  • METHOXYSUCCINYL-ALA-ALA-PRO-VALINE BORONIC ACID INHIBITOR
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
METHOXYSUCCINYL-ALA-ALA-PRO-VALINE BORONIC ACID / Alpha-lytic protease
Similarity search - Component
Biological speciesLysobacter enzymogenes (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.15 Å
AuthorsBone, R. / Agard, D.A.
Citation
Journal: Biochemistry / Year: 1989
Title: Structural analysis of specificity: alpha-lytic protease complexes with analogues of reaction intermediates.
Authors: Bone, R. / Frank, D. / Kettner, C.A. / Agard, D.A.
#1: 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.
#2: 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.
#3: 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.
#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_ref_seq / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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.db_align_beg / _struct_ref_seq.db_align_end / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 9, 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
P: METHOXYSUCCINYL-ALA-ALA-PRO-VALINE BORONIC ACID INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4423
Polymers20,3452
Non-polymers961
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-16 kcal/mol
Surface area7780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.350, 66.350, 80.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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) / References: UniProt: P00778, alpha-lytic endopeptidase
#2: Protein/peptide METHOXYSUCCINYL-ALA-ALA-PRO-VALINE BORONIC ACID INHIBITOR


Type: Peptide-like / Class: Inhibitor / Mass: 470.325 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: METHOXYSUCCINYL-ALA-ALA-PRO-VALINE BORONIC ACID
#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
Compound detailsINHIBITORY PEPTIDE BORONIC ACIDS ARE PEPTIDE ANALOGS IN WHICH THE C-TERMINAL CARBOXYL GROUP HAS ...INHIBITORY PEPTIDE BORONIC ACIDS ARE PEPTIDE ANALOGS IN WHICH THE C-TERMINAL CARBOXYL GROUP HAS BEEN REPLACED WITH THE BORONIC ACID GROUP (B(OH)2).
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). THE INHIBITOR NUMBERING (CHAIN P, 4 - 3 - 2 - 1) IS BY ANALOGY TO PROTEASE SUBSTRATE NOMENCLATURE IN WHICH THE RESIDUE PRIOR TO THE SCISSILE BOND IS THE P 1 RESIDUE AND THE NEXT TOWARDS THE N-TERMINUS IS P 2, ETC. (SEE I.SCHECTER,A.BERGER, BIOCHEM.BIOPHYS.RES.COMM., V. 27, P. 157 (1967).)
Sequence detailsCHAIN A RESIDUE NUMBERING IS DONE BY HOMOLOGY WITH CHYMOTRYPSIN FOR RESIDUES 15A - 244 AS DESCRIBED ...CHAIN A RESIDUE NUMBERING IS DONE BY HOMOLOGY WITH CHYMOTRYPSIN FOR RESIDUES 15A - 244 AS DESCRIBED IN REFERENCE 4. CHAIN P RESIDUE NUMBERING ISDONE BY ANALOGY TO PROTEASE SUBSTRATE NOMENCLATURE IN WHICH THE RESIDUE PRIOR TO THE SCISSILE BOND IS THE P 1 RESIDUE AND THE NEXT TOWARDS THE N-TERMINUS IS P 2, ETC. SEE I.SCHECTER,A.BERGER, BIOCHEM.BIOPHYS.RES.COMM., V. 27, P. 157 (1967)

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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: 51.22 %
Crystal grow
*PLUS
pH: 6.8 / Method: vapor diffusion, hanging drop
Details: seeding, refer to Bone, R. et al (1987). Biochemistry, 27, 7609-7614.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.3 M1dropLi2SO4
220 mMTris-sulphate1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.15 Å
Reflection
*PLUS
% possible obs: 89 %

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.142 / Highest resolution: 2.15 Å
Details: THE METHOXYSUCCINYL PORTION OF THE INHIBITOR WAS DISORDERED AND NO COORDINATES ARE INCLUDED FOR IT IN THIS ENTRY
Refinement stepCycle: LAST / Highest resolution: 2.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1416 0 5 141 1562
Refinement
*PLUS
σ(I): 3 / Highest resolution: 2.15 Å / Rfactor obs: 0.142
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_bond_d / Dev ideal: 0.14

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