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Yorodumi- PDB-1bxq: ACID PROTEINASE (PENICILLOPEPSIN) COMPLEX WITH PHOSPHONATE INHIBITOR. -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bxq | ||||||
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Title | ACID PROTEINASE (PENICILLOPEPSIN) COMPLEX WITH PHOSPHONATE INHIBITOR. | ||||||
Components | PROTEIN (PENICILLOPEPSIN) | ||||||
Keywords | HYDROLASE / PHOSPHONATE INHIBITORS | ||||||
Function / homology | Function and homology information penicillopepsin / aspartic-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Penicillium janthinellum (fungus) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 1.41 Å | ||||||
Authors | Parrish, J.C. / Khan, A.R. / Fraser, M.E. / Smith, W.W. / Bartlett, P.A. / James, M.N.G. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Lowering the entropic barrier for binding conformationally flexible inhibitors to enzymes. Authors: Khan, A.R. / Parrish, J.C. / Fraser, M.E. / Smith, W.W. / Bartlett, P.A. / James, M.N. #1: Journal: J.Am.Chem.Soc. / Year: 1998 Title: Macrocyclic Inhibitors of Penicillopepsin. 3. Design, Synthesis, and Evaluation of an Inhibitor Bridged between P2 and P1' Authors: Smith, W.W. / Bartlett, P.A. #2: Journal: J.Am.Chem.Soc. / Year: 1998 Title: Macrocyclic Inhibitors of Penicillopepsin. 2.X-Ray Crystallographic Analyses of Penicillopepsin Complexed with a P3-P1 Macrocyclic Peptidyl Inhibitor and with its Two Acyclic Analogues Authors: Ding, J. / Fraser, M.E. / Meyer, J.H. / Bartlett, P.A. / 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 | 1bxq.cif.gz | 85.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bxq.ent.gz | 61.9 KB | Display | PDB format |
PDBx/mmJSON format | 1bxq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/1bxq ftp://data.pdbj.org/pub/pdb/validation_reports/bx/1bxq | HTTPS FTP |
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-Related structure data
Related structure data | 1bxoC 1pplS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 33468.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Penicillium janthinellum (fungus) / References: UniProt: P00798, penicillopepsin |
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#2: Sugar |
-Non-polymers , 5 types, 412 molecules
#3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Chemical | ChemComp-PP8 / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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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: 1.51 Å3/Da / Density % sol: 18.4 % | ||||||||||||||||||||
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Crystal grow | pH: 4.6 / Details: 0.1 M CH3COONA 35% SATD. AMMONIUM SULPHATE PH 4.6 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Feb 15, 1998 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→8 Å / Num. obs: 45997 / % possible obs: 94.8 % / Redundancy: 2.33 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 56.035 |
Reflection shell | Resolution: 1.45→1.49 Å / Redundancy: 1.31 % / Rmerge(I) obs: 0.0938 / Mean I/σ(I) obs: 13.26 / % possible all: 66.3 |
Reflection | *PLUS Num. measured all: 107304 |
Reflection shell | *PLUS % possible obs: 66.3 % |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: 1PPL Resolution: 1.41→10 Å / Num. parameters: 11619 / Num. restraintsaints: 10360 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 10 / Occupancy sum hydrogen: 2279.3 / Occupancy sum non hydrogen: 2861.7 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.41→10 Å
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Refine LS restraints |
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