[English] 日本語
![](img/lk-miru.gif)
- PDB-1gbi: ALPHA-LYTIC PROTEASE WITH MET 190 REPLACED BY ALA AND GLY 216 REP... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1gbi | ||||||
---|---|---|---|---|---|---|---|
Title | ALPHA-LYTIC PROTEASE WITH MET 190 REPLACED BY ALA AND GLY 216 REPLACED BY LEU COMPLEX WITH METHOXYSUCCINYL-ALA-ALA-PRO-PHENYLALANINE BORONIC ACID | ||||||
![]() |
| ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / ACTIVE-SITE MUTATION / SERINE PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | ![]() alpha-lytic endopeptidase / serine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Mace, J.E. / Agard, D.A. | ||||||
![]() | ![]() Title: Kinetic and structural characterization of mutations of glycine 216 in alpha-lytic protease: a new target for engineering substrate specificity. Authors: Mace, J.E. / Agard, D.A. #1: ![]() Title: Structural Basis for Broad Specificity in Alpha-Lytic Protease Authors: Bone, R. / Fujushige, A. / Kettner, C.A. / Agard, D.A. #2: ![]() Title: Structural Plasticity Broadens the Specificity of an Engineered Protease Authors: Bone, R. / Silen, J.L. / Agard, D.A. #3: ![]() Title: Structural Analysis of Specificity: Alpha-Lytic Protease Complexes with Analogues of Reaction Intermediates Authors: Bone, R. / Frank, D. / Kettner, D. / Agard, D.A. #4: ![]() Title: Serine Protease Mechanism: Structure of an Inhibitory Complex of Alpha-Lytic Protease and a Tightly Bound Peptide Boronic Acid Authors: Bone, R. / Shenvi, A.B. / Kettner, C.A. / Agard, D.A. #5: ![]() Title: Refined Structure of Alpha-Lytic Protease at 1.7 Angstroms Resolution. Analysis of Hydrogen Bonding and Solvent Structure Authors: Fujinaga, M. / Delbaere, L.T.J. / Brayer, G.D. / James, M.N.G. #6: ![]() Title: Molecular Structure of the Alpha-Lytic Protease from Myxobacter 495 at 2.8 Angstroms Resolution Authors: Brayer, G.D. / Delbaere, L.T.J. / James, M.N.G. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 50.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 38.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 433.7 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gbaC ![]() 1gbbC ![]() 1gbcC ![]() 1gbdC ![]() 1gbeC ![]() 1gbfC ![]() 1gbhC ![]() 1gbjC ![]() 1gbkC ![]() 1gblC ![]() 1gbmC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 19871.121 Da / Num. of mol.: 1 / Mutation: M190A, G216L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
---|---|---|---|---|---|---|---|
#2: Protein/peptide | | ||||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | INHIBITORY PEPTIDE BORONIC ACIDS ARE PEPTIDE ANALOGS IN WHICH THE C-TERMINAL CARBOXYL GROUP HAS ...INHIBITORY | Sequence details | CHAIN A RESIDUE NUMBERING IS DONE BY HOMOLOGY WITH CHYMOTRYPSIN FOR RESIDUES 15A - 245. CHAIN P ...CHAIN A RESIDUE NUMBERING IS DONE BY HOMOLOGY WITH CHYMOTRYPS | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.11 % | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal | *PLUS Density % sol: 48.7 % | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction source | Wavelength: 1.5418 |
---|---|
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Sep 25, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→17.5 Å / Num. obs: 6917 / % possible obs: 75 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.3→17.5 Å / σ(F): 2 Details: THE METHOXYSUCCINYL PORTION OF THE INHIBITOR WAS DISORDERED AND NO COORDINATES ARE INCLUDED FOR IT IN THIS ENTRY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→17.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|