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- PDB-2wks: Structure of Helicobacter pylori Type II Dehydroquinase with a ne... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wks | ||||||
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Title | Structure of Helicobacter pylori Type II Dehydroquinase with a new carbasugar-thiophene inhibitor. | ||||||
![]() | 3-DEHYDROQUINATE DEHYDRATASE | ||||||
![]() | LYASE / AROMATIC AMINO ACID BIOSYNTHESIS / SHIKIMIC ACID PATHWAY / 3-DEHYDROQUINATE DEHYDRATASE | ||||||
Function / homology | ![]() quinate catabolic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Otero, J.M. / Guardado-Calvo, P. / Llamas-Saiz, A.L. / Prazeres, V.F.V. / Tizon, L. / Castedo, L. / Lamb, H. / Hawkins, A.R. / Gonzalez-Bello, C. / van Raaij, M.J. | ||||||
![]() | ![]() Title: Synthesis and biological evaluation of new nanomolar competitive inhibitors of Helicobacter pylori type II dehydroquinase. Structural details of the role of the aromatic moieties with essential residues. Authors: Prazeres, V.F. / Tizon, L. / Otero, J.M. / Guardado-Calvo, P. / Llamas-Saiz, A.L. / van Raaij, M.J. / Castedo, L. / Lamb, H. / Hawkins, A.R. / Gonzalez-Bello, C. #1: Journal: Med.Res.Rev. / Year: 2007 Title: Progress in Type II Dehydroquinase Inhibitors: From Concept to Practice. Authors: Gonzalez-Bello, C. / Castedo, L. #2: Journal: Chemmedchem / Year: 2008 Title: Competitive Inhibitors of Helicobacter Pylori Type II Dehydroquinase: Synthesis, Biological Evaluation, and NMR Studies. Authors: Prazeres, V.F.V. / Sanchez-Sixto, C. / Castedo, L. / Shuh, S.W. / Lamb, H. / Hawkins, A.R. / Canada, F.J. / Jimenez-Barbero, J. / Gonzalez-Bello, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 186.8 KB | Display | ![]() |
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PDB format | ![]() | 151.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2c4vS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 1 - 153 / Label seq-ID: 1 - 153
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Components
#1: Protein | Mass: 18499.246 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CB6 / ( #3: Water | ChemComp-HOH / | |
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-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: 5 Details: 26% (W/V) POLYETHYLENEGLYCOL 4000, 0.1 M 2-(N-MORPHOLINO)ETHANESULFONIC ACID-SODIUM HYDROXIDE PH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Dec 14, 2008 / Details: BENT, VERTICALLY FOCUSSING MIRROR |
Radiation | Monochromator: GE(111) TRIANGULAR BENT COMPRESSING 7O FANKUCHEN CUT Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.815 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→31 Å / Num. obs: 25927 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 74.9 Å2 / Rmerge(I) obs: 0.1 |
Reflection shell | Resolution: 2.95→3.11 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.39 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2C4V Resolution: 2.95→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.902 / SU B: 16.444 / SU ML: 0.296 / Cross valid method: THROUGHOUT / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 52.234 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→20 Å
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Refine LS restraints |
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