[English] 日本語
Yorodumi- PDB-1thl: Thermolysin complexed with a novel glutaramide derivative, n-(1-(... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1thl | ||||||
---|---|---|---|---|---|---|---|
Title | Thermolysin complexed with a novel glutaramide derivative, n-(1-(2(r,s)-carboxy-4-phenylbutyl) cyclopentylcarbonyl)-(s)-tryptophan | ||||||
Components | THERMOLYSIN | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / METALLOPROTEINASE / GLUTARAMIDE DERIVATIVE / THERMOLYSIN / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus thermoproteolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||
Authors | Holland, D.R. / Matthews, B.W. | ||||||
Citation | Journal: Biochemistry / Year: 1994 Title: Inhibition of Thermolysin and Neutral Endopeptidase 24.11 By a Novel Glutaramide Derivative; X-Ray Structure Determination of the Thermolysin-Inhibitor Complex Authors: Holland, D.R. / Barclay, P.L. / Danilewicz, J.C. / Matthews, B.W. / James, K. #1: Journal: Biochemistry / Year: 1984 Title: Binding of N-Carboxymethyl Dipeptide Inhibitors to Thermolysin Determined by X-Ray Crystallography: A Novel Class of Transition-State Analogues for Zinc Peptidases Authors: Monzingo, A.F. / Matthews, B.W. #2: Journal: J.Mol.Biol. / Year: 1982 Title: Structure of Thermolysin Refined at 1.6 Angstroms Resolution Authors: Holmes, M.A. / Matthews, B.W. #3: Journal: J.Biol.Chem. / Year: 1974 Title: The Conformation of Thermolysin Authors: Matthews, B.W. / Weaver, L.H. / Kester, W.R. #4: Journal: Nature New Biol. / Year: 1972 Title: Structure of Thermolysin Authors: Matthews, B.W. / Colman, P.M. / Jansonius, J.N. / Titani, K. / Walsh, K.A. / Neura, H. #5: Journal: Nature New Biol. / Year: 1972 Title: Three Dimensional Structure of Thermolysin Authors: Matthews, B.W. / Jansonius, J.N. / Colman, P.N. / Schoenborn, B.P. / Duporque, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1thl.cif.gz | 81.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1thl.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 1thl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1thl_validation.pdf.gz | 816.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1thl_full_validation.pdf.gz | 826.2 KB | Display | |
Data in XML | 1thl_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 1thl_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/1thl ftp://data.pdbj.org/pub/pdb/validation_reports/th/1thl | HTTPS FTP |
-Related structure data
Related structure data | 3tln S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: CIS PROLINE - PRO 51 |
-Components
#1: Protein | Mass: 34362.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin | ||||||||
---|---|---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-0DB / | #5: Water | ChemComp-HOH / | Sequence details | THE DENSITY AT POSITION 177 CLEARLY SHOWS RESIDUE GLU, NOT LYS. AUTHORS MAINTAIN THAT THE SWISSPROT ...THE DENSITY AT POSITION 177 CLEARLY SHOWS RESIDUE GLU, NOT LYS. AUTHORS MAINTAIN THAT THE SWISSPROT REFERENCE P00800 IS LIKELY TO BE INCORRECT AT THIS POSITION | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49 % |
---|---|
Crystal grow | Temperature: 277 K / pH: 7.2 Details: TRIS ACETATE, CALCIUM ACETATE, DMSO, PH 7.2, DILUTION WITH H2O, TEMPERATURE 277K |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: 1991 / Details: GRAPHITE MONOCHROMATOR, COLLIMATING SLITS |
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: 1.58→35 Å / Num. obs: 41090 / % possible obs: 86 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 12.5 Å2 / Rmerge(I) obs: 0.066 |
Reflection | *PLUS Highest resolution: 1.6 Å / Num. obs: 34103 / Rmerge(I) obs: 0.066 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3TLN 3tln Resolution: 1.7→10 Å / Isotropic thermal model: ISOTROPIC / σ(F): 0 / Stereochemistry target values: TNT VERSION 1.0
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 10 Å / Num. reflection obs: 33922 / Rfactor obs: 0.162 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|