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- PDB-2x5o: Discovery of Novel 5-Benzylidenerhodanine- and 5-Benzylidene- thi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2x5o | ||||||
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Title | Discovery of Novel 5-Benzylidenerhodanine- and 5-Benzylidene- thiazolidine-2,4-dione Inhibitors of MurD Ligase | ||||||
![]() | UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE | ||||||
![]() | LIGASE / ATP-BINDING / CELL CYCLE / CELL DIVISION / CELL SHAPE / CELL WALL BIOGENESIS/DEGRADATION / PEPTIDOGLYCAN SYNTHESIS | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Zidar, N. / Tomasic, T. / Sink, R. / Rupnik, V. / Kovac, A. / Turk, S. / Contreras-Martel, C. / Dessen, A. / Blanot, D. / Gobec, S. ...Zidar, N. / Tomasic, T. / Sink, R. / Rupnik, V. / Kovac, A. / Turk, S. / Contreras-Martel, C. / Dessen, A. / Blanot, D. / Gobec, S. / Zega, A. / Peterlin-Masic, L. / Kikelja, D. | ||||||
![]() | ![]() Title: Discovery of novel 5-benzylidenerhodanine and 5-benzylidenethiazolidine-2,4-dione inhibitors of MurD ligase. Authors: Zidar, N. / Tomasic, T. / Sink, R. / Rupnik, V. / Kovac, A. / Turk, S. / Patin, D. / Blanot, D. / Contreras Martel, C. / Dessen, A. / Muller Premru, M. / Zega, A. / Gobec, S. / Peterlin Masic, L. / Kikelj, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 193.5 KB | Display | ![]() |
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PDB format | ![]() | 152.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 733 KB | Display | ![]() |
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Full document | ![]() | 740.2 KB | Display | |
Data in XML | ![]() | 24.4 KB | Display | |
Data in CIF | ![]() | 37.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wjpC ![]() 3uagS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 47157.480 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-438 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P14900, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase |
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-Non-polymers , 6 types, 544 molecules ![](data/chem/img/VSV.gif)
![](data/chem/img/AZI.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/SO3.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/AZI.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/SO3.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-VSV / | ||||||
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#3: Chemical | ChemComp-AZI / | ||||||
#4: Chemical | #5: Chemical | ChemComp-SO3 / | #6: Chemical | ChemComp-CL / #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 1.8 M (NH4)2SO4, 7% PEG 400, 100 MM NACL, 100MM HEPES, PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 14, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→47.36 Å / Num. obs: 93804 / % possible obs: 86.2 % / Observed criterion σ(I): 3 / Redundancy: 5.2 % / Biso Wilson estimate: 24.226 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 29 |
Reflection shell | Resolution: 1.46→1.55 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3 / % possible all: 52 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3UAG Resolution: 1.46→47.36 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.805 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.46→47.36 Å
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Refine LS restraints |
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