[English] 日本語
![](img/lk-miru.gif)
- PDB-1q7g: Homoserine Dehydrogenase in complex with suicide inhibitor comple... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1q7g | ||||||
---|---|---|---|---|---|---|---|
Title | Homoserine Dehydrogenase in complex with suicide inhibitor complex NAD-5-hydroxy-4-Oxonorvaline | ||||||
![]() | Homoserine dehydrogenase | ||||||
![]() | OXIDOREDUCTASE | ||||||
Function / homology | ![]() aspartate family amino acid biosynthetic process / aspartate kinase activity / homoserine dehydrogenase / homoserine dehydrogenase activity / homoserine biosynthetic process / threonine biosynthetic process / methionine biosynthetic process / isoleucine biosynthetic process / NADP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jacques, S.L. / Mirza, I.A. / Ejim, L. / Koteva, K. / Hughes, D.W. / Green, K. / Kinach, R. / Honek, J.F. / Lai, H.K. / Berghuis, A.M. / Wright, G.D. | ||||||
![]() | ![]() Title: Enzyme assisted suicide: Molecular basis for the antifungal activity of 5-hydroxy-4-oxonorvaline by potent inhibition of homoserine dehydrogenase Authors: Jacques, S.L. / Mirza, I.A. / Ejim, L. / Koteva, K. / Hughes, D.W. / Green, K. / Kinach, R. / Honek, J.F. / Lai, H.K. / Berghuis, A.M. / Wright, G.D. | ||||||
History |
| ||||||
Remark 600 | HETEROGEN Two possible adducts were constructed differing in chirality at the HON C5 position and ...HETEROGEN Two possible adducts were constructed differing in chirality at the HON C5 position and modeled into the active site. Subsequent electron density maps and monitoring of Rfree did not indicate a convincing preference for either configuration, and thus the current model describes the chirality of the HON C5 to be 50% S and 50% R. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 147.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 116.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1020.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 30.8 KB | Display | |
Data in CIF | ![]() | 41.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ebfS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 38544.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: HOM6, YJR139C OR J2132 / Plasmid: pet22b / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-NHO / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.39 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: Sodium Acetate, Ammonium Sulfate, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: DeLaBarre, B., (1998) Acta Crystallogr., Sect.D, 54, 413. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 218 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 28, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0722 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→99 Å / Num. all: 24854 / Num. obs: 24854 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.081 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.257 / % possible all: 72 |
Reflection shell | *PLUS % possible obs: 72 % / Mean I/σ(I) obs: 4 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EBF Resolution: 2.6→40.43 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 125946.93 / Data cutoff high rms absF: 125946.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.9335 Å2 / ksol: 0.389643 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.4 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→40.43 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Rfactor Rfree: 0.295 / Rfactor Rwork: 0.232 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|