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- PDB-2vtd: Crystal structure of MurD ligase in complex with D-Glu containing... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vtd | ||||||
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Title | Crystal structure of MurD ligase in complex with D-Glu containing sulfonamide inhibitor | ||||||
![]() | UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE | ||||||
![]() | LIGASE / MURD-INHIBITOR COMPLEX / PEPTIDOGLYCAN SYNTHESIS / NUCLEOTIDE-BINDING / SULFONAMIDE INHIBITOR / MURD LIGASE / ATP-BINDING / CELL DIVISION / CYTOPLASM / CELL SHAPE / CELL CYCLE / CELL WALL BIOGENESIS/DEGRADATION | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Humljan, J. / Kotnik, M. / Contreras-Martel, C. / Blanot, D. / Urleb, U. / Dessen, A. / Solmajer, T. / Gobec, S. | ||||||
![]() | ![]() Title: Novel naphthalene-N-sulfonyl-D-glutamic acid derivatives as inhibitors of MurD, a key peptidoglycan biosynthesis enzyme. Authors: Humljan, J. / Kotnik, M. / Contreras-Martel, C. / Blanot, D. / Urleb, U. / Dessen, A. / Solmajer, T. / Gobec, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105 KB | Display | ![]() |
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PDB format | ![]() | 77.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 730.3 KB | Display | ![]() |
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Full document | ![]() | 734.5 KB | Display | |
Data in XML | ![]() | 20.9 KB | Display | |
Data in CIF | ![]() | 31.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2uuoC ![]() 2uupC ![]() 2vteC ![]() 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
#1: Protein | Mass: 47979.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: INHIBITOR N-(6-(4-CYANO-2-FLUORO-BENZYLOXY)-NAPHTHALENE-2-SULFONYL)-D-GLUTAMIC ACID BOUND Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P14900, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase |
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#2: Chemical | ChemComp-LKM / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Sequence details | C-TERMINAL HIS-TAG (SHHHHHH) |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: PROTEIN WAS CRYSTALLIZED FROM 1.7 M (NH4)2SO4, 7% PEG 400, 100 MM HEPES, PH 7.5; THEN SOAKED IN 2 MM OF INHIBITOR SOLUTION |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 30, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97623 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→50 Å / Num. obs: 39330 / % possible obs: 94.5 % / Observed criterion σ(I): 3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 24 |
Reflection shell | Resolution: 1.94→2.06 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 5 / % possible all: 88 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3UAG Resolution: 1.94→46.88 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE EXPERIMENT - - GLY A 222, ALA A 223, ASP A 224, GLN A 242, GLN A 243. RESIDUES ARG A 221 AND ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE EXPERIMENT - - GLY A 222, ALA A 223, ASP A 224, GLN A 242, GLN A 243. RESIDUES ARG A 221 AND HIS A 241 WERE MODELED AS ALANINES DUE TO INSUFFICIENT ELECTRON DENSITY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.01 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→46.88 Å
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Refine LS restraints |
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