+
Open data
-
Basic information
Entry | Database: PDB / ID: 1lne | ||||||
---|---|---|---|---|---|---|---|
Title | A STRUCTURAL ANALYSIS OF METAL SUBSTITUTIONS IN THERMOLYSIN | ||||||
![]() | THERMOLYSIN | ||||||
![]() | HYDROLASE (METALLOPROTEASE) | ||||||
Function / homology | ![]() thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Holland, D.R. / Hausrath, A.C. / Juers, D. / Matthews, B.W. | ||||||
![]() | ![]() Title: Structural analysis of zinc substitutions in the active site of thermolysin. Authors: Holland, D.R. / Hausrath, A.C. / Juers, D. / Matthews, B.W. #1: ![]() Title: Structural Comparison Suggests that Thermolysin and Related Neutral Proteases Undergo Hinge-Bending Motion During Catalysis Authors: Holland, D.R. / Tronrud, D.E. / Pley, H.W. / Flaherty, K.M. / Stark, W. / Jansonius, J.N. / Mckay, D.B. / Matthews, B.W. #2: ![]() Title: Structure of Thermolysin Refined at 1.6 Angstroms Resolution Authors: Holmes, M.A. / Matthews, B.W. #3: ![]() Title: Structure of a Mercaptan-Thermolysin Complex Illustrates Mode of Inhibition of Zinc Proteases by Substrate-Analogue Mercaptans Authors: Monzingo, A.F. / Matthews, B.W. #4: ![]() Title: Binding of Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests a Pentacoordinate Zinc Intermediate in Catalysis Authors: Holmes, M.A. / Matthews, B.W. #5: ![]() Title: Binding of the Biproduct Analog L-Benzylsuccinic Acid to Thermolysin Determined by X-Ray Crystallography Authors: Bolognesi, M.C. / Matthews, B.W. #6: ![]() Title: Comparison of the Structures of Carboxypeptidase a and Thermolysin Authors: Kester, W.R. / Matthews, B.W. #7: ![]() Title: A Crystallographic Study of the Complex of Phosphoramidon with Thermolysin. A Model for the Presumed Catalytic Transition State and for the Binding of Extended Substrates Authors: Weaver, L.H. / Kester, W.R. / Matthews, B.W. #8: ![]() Title: Crystallographic Study of the Binding of Dipeptide Inhibitors to Thermolysin. Implications for the Mechanism of Catalysis Authors: Kester, W.R. / Matthews, B.W. #9: ![]() Title: Role of Calcium in the Thermal Stability of Thermolysin Authors: Dahlquist, F.W. / Long, J.W. / Bigbee, W.L. #11: ![]() Title: Evidence of Homologous Relationship between Thermolysin and Neutral Protease a of Bacillus Subtilis Authors: Levy, P.L. / Pangburn, M.K. / Burstein, Y. / Ericsson, L.H. / Neurath, H. / Walsh, K.A. #12: ![]() Title: The Conformation of Thermolysin Authors: Matthews, B.W. / Weaver, L.H. / Kester, W.R. #13: ![]() Title: Binding of Lanthanide Ions to Thermolysin Authors: Matthews, B.W. / Weaver, L.H. #14: ![]() Title: The Structure of Thermolysin,an Electron Density Map at 2.3 Angstroms Resolution Authors: Colman, P.M. / Jansonius, J.N. / Matthews, B.W. #15: ![]() Title: Amino-Acid Sequence of Thermolysin Authors: Titani, K. / Hermodson, M.A. / Ericsson, L.H. / Walsh, K.A. / Neurath, H. #16: ![]() Title: Three Dimensional Structure of Thermolysin Authors: Matthews, B.W. / Jansonius, J.N. / Colman, P.M. / Schoenborn, B.P. / Duporque, D. #17: ![]() Title: Structure of Thermolysin Authors: Matthews, B.W. / Colman, P.M. / Jansonius, J.N. / Titani, K. / Walsh, K.A. / Neurath, H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 82.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 61.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 464 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 22.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: CIS PROLINE - PRO E 51 |
-
Components
-Protein , 1 types, 1 molecules E
#1: Protein | Mass: 34362.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P00800, thermolysin |
---|
-Non-polymers , 6 types, 163 molecules ![](data/chem/img/VAL.gif)
![](data/chem/img/LYS.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/LYS.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-VAL / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-LYS / | ||||||
#4: Chemical | ChemComp-CD / #5: Chemical | #6: Chemical | ChemComp-DMS / | #7: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | RESIDUES 1321 AND 1322 FORM A DIPEPTIDE (VAL-LYS) BOUND IN THE ACTIVE SITE OF THE MOLECULE. IT IS ...RESIDUES 1321 AND 1322 FORM A DIPEPTIDE (VAL-LYS) BOUND IN THE ACTIVE SITE OF THE MOLECULE. IT IS PRESUMED THAT THE ORIGIN OF THIS DIPEPTIDE IS THE C-TERMINAL TWO RESIDUES OF THE PROTEIN. SINCE THE C-TERMINUS APPEARS AT FULL OCCUPANCY, MOLECULES NOT INCORPORAT |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.97 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.2 / Details: pH 7.2 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown / Details: Holmes, M.A., (1982) J.Mol.Biol., 160, 623. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: XUONG-HAMLIN / Detector: MULTIWIRE AREA DETECTOR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.7 Å / % possible obs: 88 % / Rmerge(I) obs: 0.049 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR SUBSTITUTION / Resolution: 1.7→20 Å / σ(F): 0 /
| ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
| ||||||||||||||||||||||||||||||
Refine LS restraints |
|