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Yorodumi- PDB-1p11: CRYSTAL STRUCTURES OF ALPHA-LYTIC PROTEASE COMPLEXES WITH IRREVER... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p11 | |||||||||
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Title | CRYSTAL STRUCTURES OF ALPHA-LYTIC PROTEASE COMPLEXES WITH IRREVERSIBLY BOUND PHOSPHONATE ESTERS | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information alpha-lytic endopeptidase / serine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | |||||||||
Biological species | Lysobacter enzymogenes (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.93 Å | |||||||||
Authors | Bone, R. / Agard, D.A. | |||||||||
Citation | Journal: Biochemistry / Year: 1991 Title: Crystal structures of alpha-lytic protease complexes with irreversibly bound phosphonate esters. Authors: Bone, R. / Sampson, N.S. / Bartlett, P.A. / Agard, D.A. #1: Journal: Biochemistry / Year: 1991 Title: Peptidic Phosphonylating Agents as Irreversible Inhibitors of Serine Proteases and Models of the Tetrahedral Intermediates Authors: Sampson, N.S. / Bartlett, P.A. #2: 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. #3: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p11.cif.gz | 58.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p11.ent.gz | 40 KB | Display | PDB format |
PDBx/mmJSON format | 1p11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p11_validation.pdf.gz | 387.6 KB | Display | wwPDB validaton report |
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Full document | 1p11_full_validation.pdf.gz | 392.9 KB | Display | |
Data in XML | 1p11_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 1p11_validation.cif.gz | 10.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/1p11 ftp://data.pdbj.org/pub/pdb/validation_reports/p1/1p11 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: PRO E 99A IS A CIS PROLINE. / 2: SEE REMARK 5. / 3: SEE REMARK 6. |
-Components
#1: Protein | Mass: 19875.131 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lysobacter enzymogenes (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P00778, alpha-lytic endopeptidase |
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#2: Protein/peptide | Type: Peptide-like / Class: Inhibitor / Mass: 635.644 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source References: N-(tert-butoxycarbonyl)-L-alanyl-L-alanyl-N-{(1R)-1-[(S)-[(1S)-2-{[(1R)-1-carboxyethyl]amino}-1-methyl-2-oxoethoxy](hyd roxy)phosphoryl]-2-methylpropyl}-L-prolinamide |
#3: Protein/peptide | |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
Compound details | THE PVA RESIDUE IN THE INHIBITOR IS THE ALPHA-AMINO PHOSPHONIC ACID ANALOG OF VAL IN WHICH THE C- ...THE PVA RESIDUE IN THE INHIBITOR IS THE ALPHA-AMINO PHOSPHONIC |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.55 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||
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Refinement | Rfactor obs: 0.128 / Highest resolution: 1.93 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.93 Å
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Refinement | *PLUS σ(I): 3 / Rfactor obs: 0.127 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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