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Yorodumi- PDB-1lcp: BOVINE LENS LEUCINE AMINOPEPTIDASE COMPLEXED WITH L-LEUCINE PHOSP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lcp | ||||||
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Title | BOVINE LENS LEUCINE AMINOPEPTIDASE COMPLEXED WITH L-LEUCINE PHOSPHONIC ACID | ||||||
Components | LEUCINE AMINOPEPTIDASELeucyl aminopeptidase | ||||||
Keywords | HYDROLASE (ALPHA-AMINOACYLPEPTIDE) | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.65 Å | ||||||
Authors | Straeter, N. / Lipscomb, W.N. | ||||||
Citation | Journal: Biochemistry / Year: 1995 Title: Transition state analogue L-leucinephosphonic acid bound to bovine lens leucine aminopeptidase: X-ray structure at 1.65 A resolution in a new crystal form. Authors: Strater, N. / Lipscomb, W.N. #1: Journal: Adv.Enzymol.Relat.Areas Mol.Biol. / Year: 1994 Title: Structure and Mechanism of Bovine Lens Leucine Aminopeptidase Authors: Kim, H. / Lipscomb, W.N. #2: 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. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993 Title: Differentiation and Identification of the Two Catalytic Metal Binding Sites in Bovine Lens Leucine Aminopeptidase by X-Ray Crystallography Authors: Kim, H. / Lipscomb, W.N. #4: 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. #5: 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. #6: 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 | 1lcp.cif.gz | 217.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lcp.ent.gz | 173.2 KB | Display | PDB format |
PDBx/mmJSON format | 1lcp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/1lcp ftp://data.pdbj.org/pub/pdb/validation_reports/lc/1lcp | 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 A 471 / 2: CIS PROLINE - PRO B 471 | |||||||||
Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.998453, -0.054621, 0.010423), Vector: Details | MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 B 1 .. 484 A 1 .. 484 0.218 SYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. APPLIED TO RESIDUES: A 1 .. 490 1 OF 4 TRANSFORMATIONS TO GENERATE ONE HEXAMER OF 32 SYMMETRY. SYMMETRY1 1 -0.500000 -0.866025 0.000000 65.15000 SYMMETRY2 1 0.866025 -0.500000 0.000000 112.84310 SYMMETRY3 1 0.000000 0.000000 1.000000 0.00000 APPLIED TO RESIDUES: A 1 .. 490 1 OF 4 TRANSFORMATIONS TO GENERATE ONE HEXAMER OF 32 SYMMETRY. SYMMETRY1 2 -0.500000 0.866025 0.000000 -65.15000 SYMMETRY2 2 -0.866025 -0.500000 0.000000 112.84310 SYMMETRY3 2 0.000000 0.000000 1.000000 0.00000 APPLIED TO RESIDUES: B 1 .. 490 1 OF 4 TRANSFORMATIONS TO GENERATE ONE HEXAMER OF 32 SYMMETRY. SYMMETRY1 1 -0.500000 -0.866025 0.000000 65.15000 SYMMETRY2 1 0.866025 -0.500000 0.000000 112.84310 SYMMETRY3 1 0.000000 0.000000 1.000000 0.00000 APPLIED TO RESIDUES: B 1 .. 490 1 OF 4 TRANSFORMATIONS TO GENERATE ONE HEXAMER OF 32 SYMMETRY. SYMMETRY1 2 -0.500000 0.866025 0.000000 -65.15000 SYMMETRY2 2 -0.866025 -0.500000 0.000000 112.84310 SYMMETRY3 2 0.000000 0.000000 1.000000 0.00000 | |
-Components
#1: Protein | Mass: 52668.855 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: EYE LENSLens (anatomy) / References: UniProt: P00727, leucyl aminopeptidase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-MRD / ( #5: Water | ChemComp-HOH / | Compound details | THE SECONDARY STRUCTURE ASSIGNMENT IS TAKEN FROM REFERENCE 3. THERE ARE NO SIGNIFICANT DEVIATIONS ...THE SECONDARY STRUCTURE ASSIGNMENT | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.88 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 Å |
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Detector | Type: XENTRONICS / Detector: AREA DETECTOR / Date: Dec 8, 1994 |
Radiation | Monochromator: SUPPER DOUBLE MIRROR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→36 Å / Num. obs: 144211 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.074 |
Reflection | *PLUS Num. measured all: 766198 / Rmerge(I) obs: 0.074 |
-Processing
Software |
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Refinement | Resolution: 1.65→7 Å / σ(F): 2 Details: ALL WATER MOLECULES EXCEPT OF 4 HAVE BEEN REFINED WITH THE PARAM19.SOL PARAMETER FILE IN X-PLOR 3.1. THE FOUR ACTIVE SITE WATER MOLECULES 967, 968, 969, AND 970 HAVE BEEN REFINED TURNING OFF ...Details: ALL WATER MOLECULES EXCEPT OF 4 HAVE BEEN REFINED WITH THE PARAM19.SOL PARAMETER FILE IN X-PLOR 3.1. THE FOUR ACTIVE SITE WATER MOLECULES 967, 968, 969, AND 970 HAVE BEEN REFINED TURNING OFF NON-BONDED INTERACTIONS WITH EACH OTHER IN ORDER TO GET A NON-BIASED VALUE OF THE SHORT DISTANCE BETWEEN WATER MOLECULES 967 AND 968 (2.3 ANG) AND BETWEEN 969 AND 970 (2.1 ANG).
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Displacement parameters | Biso mean: 12.7 Å2 | ||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.17 Å | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→7 Å
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.16 / Rfactor Rwork: 0.16 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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