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- PDB-7pzw: LpxC Inhibitors With Fluoroproline As A Novel Zinc-Binding Group ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7pzw | ||||||
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Title | LpxC Inhibitors With Fluoroproline As A Novel Zinc-Binding Group Can Serve As A Novel Class of Antibiotic With Activity Against Multidrug-Resistant Gram-Negative Bacteria | ||||||
![]() | UDP-3-O-acyl-N-acetylglucosamine deacetylase | ||||||
![]() | HYDROLASE / Elastase / Inhibitor / Fluoroproline / Zinc-Binding Group / Antibiotic / Multidrug-Resistant Gram-Negative Bacteria | ||||||
Function / homology | ![]() UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity / UDP-3-O-acyl-N-acetylglucosamine deacetylase activity / lipid A biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ryan, M.D. / Pallin, T.D. / Lamers, M.B.A.C. / Leonard, P.M. | ||||||
Funding support | 1items
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![]() | ![]() Title: LpxC Inhibitors With Fluoroproline As A Novel Zinc-Binding Group Can Serve As A Novel Class of Antibiotic With Activity Against Multidrug-Resistant Gram-Negative Bacteria Authors: Ryan, M.D. / Pallin, T.D. / Mullins, T. / Blench, T. / Fraser, I. / Dallow, J. / Ahmed, N. / Ellwood, C. / Gaines, S. / Flores, J. / Blackwell, Y. / Garcia, C.T. / Spence, G. / Reeve, A. / ...Authors: Ryan, M.D. / Pallin, T.D. / Mullins, T. / Blench, T. / Fraser, I. / Dallow, J. / Ahmed, N. / Ellwood, C. / Gaines, S. / Flores, J. / Blackwell, Y. / Garcia, C.T. / Spence, G. / Reeve, A. / Panchal, T. / Dominguez-Fernandez, B. / Leonard, P.M. / Lamers, M.B.A.C. / Arduin, A. / Fotinou, C. / Gancia, E. / Clark, D.E. / Bush, E. / Betts, J. / Richards, C. / Rea-Davies, T. / Keefe, A.D. / Zhang, Y. / Soutter, H.T. / Centrella, P.A. / Clark, M.A. / Cuozzo, J.W. / Dumelin, C.E. / Habeshian, S. / Hunt, A. / Sigel, E.A. / Troast, D.M. / DeJonge, B.L.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.4 KB | Display | ![]() |
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PDB format | ![]() | 55.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7phjC ![]() 7phnC ![]() 7pj2C ![]() 7pjgC ![]() 7pk8C ![]() 7pkkC ![]() 7pkmC ![]() 7pzsC ![]() 7pzuC ![]() 7pzvC ![]() 7pzxC ![]() 7q01C ![]() 2vesS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 34857.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: lpxC, envA, PA4406 / Production host: ![]() ![]() References: UniProt: P47205, UDP-3-O-acyl-N-acetylglucosamine deacetylase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-9A1 / ( |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 26% PEG 3350, 0.2 M NA FORMATE |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2→62.87 Å / Num. obs: 19507 / % possible obs: 98.3 % / Redundancy: 3.4 % / CC1/2: 0.99 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 2→2.05 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1421 / CC1/2: 0.438 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2VES Resolution: 2→62.87 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.51 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.234 Å2
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Refinement step | Cycle: 1 / Resolution: 2→62.87 Å
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Refine LS restraints |
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