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- PDB-1ek6: STRUCTURE OF HUMAN UDP-GALACTOSE 4-EPIMERASE COMPLEXED WITH NADH ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ek6 | ||||||
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Title | STRUCTURE OF HUMAN UDP-GALACTOSE 4-EPIMERASE COMPLEXED WITH NADH AND UDP-GLUCOSE | ||||||
![]() | UDP-GALACTOSE 4-EPIMERASE | ||||||
![]() | ISOMERASE / Epimerase / Short-Chain Dehydrogenase / Galactosemia | ||||||
Function / homology | ![]() Defective GALE causes EDG / UDP-N-acetylglucosamine 4-epimerase / UDP-N-acetylglucosamine 4-epimerase activity / galactose catabolic process / Galactose catabolism / UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose catabolic process via UDP-galactose / protein homodimerization activity / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Thoden, J.B. / Wohlers, T.M. / Fridovich-Keil, J.L. / Holden, H.M. | ||||||
![]() | ![]() Title: Crystallographic evidence for Tyr 157 functioning as the active site base in human UDP-galactose 4-epimerase. Authors: Thoden, J.B. / Wohlers, T.M. / Fridovich-Keil, J.L. / Holden, H.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 | ![]() | 174.5 KB | Display | ![]() |
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PDB format | ![]() | 135 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 38.9 KB | Display | |
Data in CIF | ![]() | 59.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | homodimer constructed from chains A & B |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 38324.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 908 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/UPG.gif)
![](data/chem/img/TMA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/UPG.gif)
![](data/chem/img/TMA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.02 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 273 K / Method: batch / pH: 6 Details: PEG 3400, magnesium chloride, MES, NADH, UDP-glucose, sodium chloride, pH 6.0, BATCH, temperature 273.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SBC-2 / Detector: CCD / Date: Dec 21, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. all: 96156 / Num. obs: 96156 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 29.9 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.286 / Num. unique all: 8401 / % possible all: 84.7 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 84.7 % / Num. unique obs: 8401 / Mean I/σ(I) obs: 2.9 |
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Processing
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Refinement | Resolution: 1.5→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 96012 / σ(F): 0 / Rfactor all: 0.169 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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