[English] 日本語
![](img/lk-miru.gif)
- PDB-2y68: Structure-based design of a new series of D-glutamic acid-based i... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2y68 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure-based design of a new series of D-glutamic acid-based inhibitors of bacterial MurD ligase | ||||||
![]() | UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE | ||||||
![]() | LIGASE / ATP-BINDING / CELL CYCLE / CELL DIVISION / CELL SHAPE / CELL WALL / CELL WALL BIOGENESIS/DEGRADATION / NUCLEOTIDE-BINDING / PEPTIDOGLYCAN SYNTHESIS / UMA | ||||||
Function / homology | ![]() UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase / UDP-N-acetylmuramoylalanine-D-glutamate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tomasic, T. / Zidar, N. / Sink, R. / Kovac, A. / Patin, D. / Blanot, D. / Contreras-Martel, C. / Dessen, A. / Muller-Premru, M. / Zega, A. ...Tomasic, T. / Zidar, N. / Sink, R. / Kovac, A. / Patin, D. / Blanot, D. / Contreras-Martel, C. / Dessen, A. / Muller-Premru, M. / Zega, A. / Gobec, S. / Peterlin-Masic, L. / Kikelj, D. | ||||||
![]() | ![]() Title: Structure-based design of a new series of D-glutamic acid based inhibitors of bacterial UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (MurD). Authors: Tomasic, T. / Zidar, N. / Sink, R. / Kovac, A. / Blanot, D. / Contreras-Martel, C. / Dessen, A. / Muller-Premru, M. / Zega, A. / Gobec, S. / Kikelj, D. / Masic, L.P. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 198.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 157.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 750.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 757.4 KB | Display | |
Data in XML | ![]() | 23.7 KB | Display | |
Data in CIF | ![]() | 36.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1uagS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 47979.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 / Plasmid: PABD16/MURD / Production host: ![]() ![]() References: UniProt: P14900, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase |
---|
-Non-polymers , 6 types, 463 molecules ![](data/chem/img/T04.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/AZI.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/AZI.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-T04 / | ||||||||
---|---|---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | ChemComp-AZI / #5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.27 % / Description: NONE |
---|---|
Crystal grow | pH: 7.4 Details: 6.0 MG/ML MURD, 20 MM HEPES PH 7.4, 200MM NACL, 5MM DITHIOTHREITOL, 0.05% (W/V) NAN3, 0.1M HEPES PH 7.5, 1.9 M AMMONIUM SULPHATE, 7% (W/V) PEG 400, 50 MM NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97238 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→46.35 Å / Num. obs: 88810 / % possible obs: 87.8 % / Observed criterion σ(I): 3 / Redundancy: 5.2 % / Biso Wilson estimate: 26.405 Å2 / Rsym value: 0.03 / Net I/σ(I): 34.43 |
Reflection shell | Resolution: 1.49→1.58 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 3.11 / Rsym value: 0.48 / % possible all: 60.4 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1UAG Resolution: 1.49→46.35 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.097 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.724 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.49→46.35 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|