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Yorodumi- PDB-2ch5: Crystal structure of human N-acetylglucosamine kinase in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ch5 | |||||||||
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Title | Crystal structure of human N-acetylglucosamine kinase in complex with N-acetylglucosamine | |||||||||
Components | NAGK PROTEIN | |||||||||
Keywords | TRANSFERASE / N-ACETYLGLUCOSAMINE / GLCNAC / SUGAR KINASE / RIBONUCLEASE H FOLD / SUGAR KINASE/HSP70/ACTIN SUPERFAMILY / DOMAIN ROTATION / OPEN CONFORMATION / CLOSED CONFORMATION / HYPOTHETICAL PROTEIN | |||||||||
Function / homology | Function and homology information muramyl dipeptide kinase activity / N-acetylglucosamine kinase / N-acetylglucosamine kinase activity / N-acylmannosamine kinase / N-acetylmannosamine metabolic process / Synthesis of UDP-N-acetyl-glucosamine / N-acetylglucosamine metabolic process / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / N-acetylneuraminate catabolic process ...muramyl dipeptide kinase activity / N-acetylglucosamine kinase / N-acetylglucosamine kinase activity / N-acylmannosamine kinase / N-acetylmannosamine metabolic process / Synthesis of UDP-N-acetyl-glucosamine / N-acetylglucosamine metabolic process / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / N-acetylneuraminate catabolic process / UDP-N-acetylglucosamine biosynthetic process / response to muramyl dipeptide / defense response to bacterium / innate immune response / extracellular exosome / ATP binding / cytosol Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Weihofen, W.A. / Berger, M. / Chen, H. / Saenger, W. / Hinderlich, S. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Structures of Human N-Acetylglucosamine Kinase in Two Complexes with N-Acetylglucosamine and with Adp/Glucose: Insights Into Substrate Specificity and Regulation. Authors: Weihofen, W.A. / Berger, M. / Chen, H. / Saenger, W. / Hinderlich, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ch5.cif.gz | 287.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ch5.ent.gz | 238.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ch5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/2ch5 ftp://data.pdbj.org/pub/pdb/validation_reports/ch/2ch5 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 37790.027 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) Description: CDNA FROM THE RESOURCE CENTER OF THE GERMAN HUMAN GENOME PROJECT Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q6IA84, UniProt: Q9UJ70*PLUS, N-acetylglucosamine kinase #2: Sugar | #3: Chemical | ChemComp-GOL / #4: Sugar | ChemComp-NDG / | #5: Water | ChemComp-HOH / | Sequence details | N-TERMINAL CLONING ARTEFACTS (3 RESIDUES) LINKED TO CHAINS A, B, C, D. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.8 % |
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Crystal grow | pH: 5.6 Details: 100 MM HEPES PH 7.0, 100 MM NACL, 8% (W/V) PEG 4000, 2MM GLCNAC |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 19, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→2.05 Å / Num. obs: 140534 / % possible obs: 93.3 % / Observed criterion σ(I): 2.5 / Redundancy: 1.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.9→2.05 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.5 / % possible all: 81.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HUMAN N-ACETYLGLUCOSAMINE KINASE IN COMPLEX WITH ADP AND GLUCOSE Resolution: 1.9→90.17 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.135 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 292 TO 294 OF CHAIN A, 294 TO 298 OF CHAIN B, 293 TO 297 OF CHAIN C, AND 294 TO 298 OF CHAIN D ARE PARTIALLY DISORDERED AND WERE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 292 TO 294 OF CHAIN A, 294 TO 298 OF CHAIN B, 293 TO 297 OF CHAIN C, AND 294 TO 298 OF CHAIN D ARE PARTIALLY DISORDERED AND WERE NOT MODELED DUE TO LACK OF ELECTRON DENSITY.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.16 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→90.17 Å
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