[English] 日本語

- PDB-2y71: Structure of Mycobacterium tuberculosis type II dehydroquinase co... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2y71 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Mycobacterium tuberculosis type II dehydroquinase complexed with (1R,4S,5R)-1,4,5-trihydroxy-3-((5-methylbenzo(b) thiophen-2-yl)methoxy)cyclohex-2-enecarboxylate | ||||||
![]() | 3-DEHYDROQUINATE DEHYDRATASE | ||||||
![]() | LYASE / AMINO ACID BIOSYNTHESIS | ||||||
Function / homology | ![]() quinate catabolic process / Chorismate via Shikimate Pathway / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Otero, J.M. / Llamas-Saiz, A.L. / Fox, G.C. / Tizon, L. / Prazeres, V.F.V. / Lamb, H. / Hawkins, A.R. / Ainsa, J.A. / Castedo, L. / Gonzalez-Bello, C. / van Raaij, M.J. | ||||||
![]() | ![]() Title: A prodrug approach for improving antituberculosis activity of potent Mycobacterium tuberculosis type II dehydroquinase inhibitors. Authors: Tizon, L. / Otero, J.M. / Prazeres, V.F. / Llamas-Saiz, A.L. / Fox, G.C. / van Raaij, M.J. / Lamb, H. / Hawkins, A.R. / Ainsa, J.A. / Castedo, L. / Gonzalez-Bello, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 78.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 58.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 704.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 705.3 KB | Display | |
Data in XML | ![]() | 9.5 KB | Display | |
Data in CIF | ![]() | 13 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y76C ![]() 2y77C ![]() 1h0sS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 15676.737 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A4Z6, UniProt: P9WPX7*PLUS, 3-dehydroquinate dehydratase | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-CB6 / ( | ||||||
#3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Sequence details | INITIATOR METHIONINE | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE |
---|---|
Crystal grow | pH: 7.5 Details: 32% (V/V) 2-METHYL-2, 4-PENTANEDIOL, 0.3 M AMMONIUM SULPHATE, 0.1 M HEPES-NAOH PH 7.5 . |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2010 / Details: BENT CYLINDRICAL MIRRORS |
Radiation | Monochromator: SINGLE SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→29.1 Å / Num. obs: 26866 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2 / % possible all: 99.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1H0S Resolution: 1.5→21.41 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.711 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 13.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→21.41 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|