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Yorodumi- PDB-1bll: X-RAY CRYSTALLOGRAPHIC DETERMINATION OF THE STRUCTURE OF BOVINE L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bll | |||||||||
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Title | X-RAY CRYSTALLOGRAPHIC DETERMINATION OF THE STRUCTURE OF BOVINE LENS LEUCINE AMINOPEPTIDASE COMPLEXED WITH AMASTATIN: FORMULATION OF A CATALYTIC MECHANISM FEATURING A GEM-DIOLATE TRANSITION STATE | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / ALPHA-AMINOACYLPEPTIDE / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information cysteinylglycine-S-conjugate dipeptidase / prolyl aminopeptidase / leucyl aminopeptidase / dipeptidase activity / metalloaminopeptidase activity / carboxypeptidase activity / disordered domain specific binding / manganese ion binding / peptidase activity / mitochondrion ...cysteinylglycine-S-conjugate dipeptidase / prolyl aminopeptidase / leucyl aminopeptidase / dipeptidase activity / metalloaminopeptidase activity / carboxypeptidase activity / disordered domain specific binding / manganese ion binding / peptidase activity / mitochondrion / proteolysis / cytoplasm Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) Streptomyces sp. ME98-M3 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.4 Å | |||||||||
Authors | Kim, H. / Lipscomb, W.N. | |||||||||
Citation | Journal: Biochemistry / Year: 1993 Title: X-ray crystallographic determination of the structure of bovine lens leucine aminopeptidase complexed with amastatin: formulation of a catalytic mechanism featuring a gem-diolate transition state. Authors: Kim, H. / Lipscomb, W.N. #1: Journal: J.Mol.Biol. / Year: 1992 Title: Structure Determination and Refinement of Bovine Lens Leucine Aminopeptidase and its Complex with Bestatin Authors: Burley, S.K. / David, P.R. / Sweet, R.M. / Taylor, A. / Lipscomb, W.N. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991 Title: Leucine Aminopeptidase: Bestatin Inhibition and a Model for Enzyme-Catalyzed Peptide Hydrolysis Authors: Burley, S.K. / David, P.R. / Lipscomb, W.N. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1990 Title: Molecular Structure of Leucine Aminopeptidase at 2.7 Angstroms Resolution Authors: Burley, S.K. / David, P.R. / Taylor, A. / Lipscomb, W.N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bll.cif.gz | 109.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bll.ent.gz | 82.8 KB | Display | PDB format |
PDBx/mmJSON format | 1bll.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/1bll ftp://data.pdbj.org/pub/pdb/validation_reports/bl/1bll | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO E 471 |
-Components
#1: Protein | Mass: 52968.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Tissue: LENS / References: UniProt: P00727, leucyl aminopeptidase | ||||||||
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#2: Protein/peptide | | ||||||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | THE AMASTATIN INHIBITOR, (2S,3R)3-AMINO-2-HYDROXYL-5-METHYL, -HEXANOYL-L-VAL-L-VAL-L-ASP, IS ...THE AMASTATIN INHIBITOR, (2S,3R)3-AMINO-2-HYDROXYL-5-METHYL, -HEXANOYL-L-VAL-L-VAL-L-ASP, IS PRESENTED IN THIS ENTRY AS CHAIN I | Nonpolymer details | THE AMASTATIN INHIBITOR, (2S,3R)3-AMINO-2-HYDROXYL-5-METHYL -HEXANOYL-L-VAL-L-VAL-L-ASP, IS ...THE AMASTATIN INHIBITOR, (2S,3R)3-AMINO-2-HYDROXYL-5-METHYL -HEXANOYL-L-VAL-L-VAL-L-ASP, IS PRESENTED IN THIS ENTRY AS CHAIN *I*. THE HET GROUP FOR IS A CARBOXYL LINKAGE INSERTED BETWEEN THE CARBOXY TERMINUS OF LEU I 1 AND THE AMINO TERMINUS OF VAL I 2. | Sequence details | THE AMINO ACID SEQUENCE USED IN THIS STRUCTURE DETERMINATION IS TAKEN FROM WALLNER ET AL. (1993) ...THE AMINO ACID SEQUENCE USED IN THIS STRUCTURE DETERMINAT | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.99 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
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 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 8.9 Å / Num. obs: 23316 / Rmerge(I) obs: 0.089 |
Reflection shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.48 Å / Num. unique obs: 2019 / Rmerge(I) obs: 0.183 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.198 / Rfactor obs: 0.198 / Highest resolution: 2.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.4 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / Num. reflection obs: 20436 / σ(I): 2 / Rfactor obs: 0.198 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.5 |