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- PDB-2bh9: X-RAY STRUCTURE OF A DELETION VARIANT OF HUMAN GLUCOSE 6-PHOSPHAT... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bh9 | ||||||
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Title | X-RAY STRUCTURE OF A DELETION VARIANT OF HUMAN GLUCOSE 6-PHOSPHATE DEHYDROGENASE COMPLEXED WITH STRUCTURAL AND COENZYME NADP | ||||||
![]() | GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / OXIDOREDUCTASE (CHOH(D)-NADP) / CARBOHYDRATE METABOLISM / GLUCOSE METABOLISM | ||||||
Function / homology | ![]() negative regulation of protein glutathionylation / pentose biosynthetic process / ribose phosphate biosynthetic process / glucose-6-phosphate dehydrogenase (NADP+) / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / glucose-6-phosphate dehydrogenase activity / response to iron(III) ion / Pentose phosphate pathway / pentose-phosphate shunt, oxidative branch / NADPH regeneration ...negative regulation of protein glutathionylation / pentose biosynthetic process / ribose phosphate biosynthetic process / glucose-6-phosphate dehydrogenase (NADP+) / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / glucose-6-phosphate dehydrogenase activity / response to iron(III) ion / Pentose phosphate pathway / pentose-phosphate shunt, oxidative branch / NADPH regeneration / negative regulation of cell growth involved in cardiac muscle cell development / glucose 6-phosphate metabolic process / NADP metabolic process / pentose-phosphate shunt / D-glucose binding / NFE2L2 regulates pentose phosphate pathway genes / response to food / erythrocyte maturation / cholesterol biosynthetic process / centriolar satellite / negative regulation of reactive oxygen species metabolic process / regulation of neuron apoptotic process / substantia nigra development / glutathione metabolic process / TP53 Regulates Metabolic Genes / response to organic cyclic compound / lipid metabolic process / cytoplasmic side of plasma membrane / glucose metabolic process / NADP binding / cellular response to oxidative stress / response to ethanol / intracellular membrane-bounded organelle / protein homodimerization activity / extracellular exosome / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gover, S. / Vandeputte-Rutten, L. / Au, S.W.N. / Adams, M.J. | ||||||
![]() | ![]() Title: Structural Studies of Glucose-6-Phosphate and Nadp+ Binding to Human Glucose-6-Phosphate Dehydrogenase Authors: Kotaka, M. / Gover, S. / Vandeputte-Rutten, L. / Au, S.W.N. / Lam, V.M.S. / Adams, M.J. #1: ![]() Title: Human Glucose-6-Phosphate Dehydrogenase: The Crystal Structure Reveals a Structural Nadp Molecule and Provides Insights Into Enzyme Deficiency Authors: Au, S.W.N. / Gover, S. / Lam, V.M.S. / Adams, M.J. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Solution of the Structure of Tetrameric Human Glucose 6-Phosphate Dehydrogenase by Molecular Replacement Authors: Au, S.W.N. / Naylor, C.E. / Gover, S. / Vandeputte-Rutten, L. / Scopes, D.A. / Mason, P.J. / Luzzatto, L. / Lam, V.M.S. / Adams, M.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.4 KB | Display | ![]() |
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PDB format | ![]() | 90.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 518.2 KB | Display | ![]() |
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Full document | ![]() | 543.1 KB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 22.3 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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 56397.258 Da / Num. of mol.: 1 / Fragment: RESIDUES 26-514 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P11413, glucose-6-phosphate dehydrogenase (NADP+) | ||||||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | THE G6PD USED IN THIS WORK IS AN ENGINEERED VARIANT IN WHICH THE 25 N-TERMINAL RESIDUES HAVE BEEN ...THE G6PD USED IN THIS WORK IS AN ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.4 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8 Details: HANGING DROP VAPOUR DIFFUSION. 1-PLUS-1 MICROLITRE DROPS IN THE WELL 0.1M TRIS-HCL,PH 7.5-8.2, 10-16% PEG 4000. PROTEIN CONCENTRATION 5MG/ML. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 21, 1996 / Details: MIRRORS |
Radiation | Monochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.7 Å / Num. obs: 14581 / % possible obs: 73.3 % / Observed criterion σ(I): -4 / Redundancy: 2.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.4 / % possible all: 59.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PARTIALLY-REFINED MONOMER OF HUMAN G6PD, CANTON VARIANT Resolution: 2.5→29.7 Å / Cross valid method: FREE THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.5→29.7 Å
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