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- PDB-4zcg: Crystal Structure of human GGT1 in complex with Glutamate (with a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4zcg | ||||||
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Title | Crystal Structure of human GGT1 in complex with Glutamate (with all atoms of glutamate) | ||||||
![]() | (Gamma-glutamyltranspeptidase 1 ...) x 2 | ||||||
![]() | HYDROLASE / NTN-HYDROLASE FAMILY / GLYCOPROTEIN / N- GLYCOSYLATION / CELL SURFACE | ||||||
Function / homology | ![]() leukotriene-C4 hydrolase / peptidyltransferase activity / leukotriene-C(4) hydrolase / leukotriene D4 biosynthetic process / Defective GGT1 causes GLUTH / Defective GGT1 in aflatoxin detoxification causes GLUTH / LTC4-CYSLTR mediated IL4 production / Glutathione synthesis and recycling / peptide modification / gamma-glutamyltransferase ...leukotriene-C4 hydrolase / peptidyltransferase activity / leukotriene-C(4) hydrolase / leukotriene D4 biosynthetic process / Defective GGT1 causes GLUTH / Defective GGT1 in aflatoxin detoxification causes GLUTH / LTC4-CYSLTR mediated IL4 production / Glutathione synthesis and recycling / peptide modification / gamma-glutamyltransferase / glutathione gamma-glutamate hydrolase / glutathione hydrolase activity / leukotriene C4 gamma-glutamyl transferase activity / glutathione catabolic process / glutathione biosynthetic process / leukotriene metabolic process / glutamate metabolic process / Aflatoxin activation and detoxification / cysteine biosynthetic process / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of immune system process / Paracetamol ADME / amino acid metabolic process / zymogen activation / fatty acid metabolic process / regulation of inflammatory response / spermatogenesis / proteolysis / extracellular space / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
Model details | Complex | ||||||
![]() | Terzyan, S. / Hanigan, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Human gamma-Glutamyl Transpeptidase 1: STRUCTURES OF THE FREE ENZYME, INHIBITOR-BOUND TETRAHEDRAL TRANSITION STATES, AND GLUTAMATE-BOUND ENZYME REVEAL NOVEL MOVEMENT WITHIN THE ACTIVE SITE DURING CATALYSIS. Authors: Terzyan, S.S. / Burgett, A.W. / Heroux, A. / Smith, C.A. / Mooers, B.H. / Hanigan, M.H. #1: ![]() Title: Novel insights into eukaryotic gamma-glutamyl transpeptidase 1 from the crystal structure of the glutamate-bound human enzyme. Authors: West, M. / Chen, Y. / Wickham, S. / Heroux, A. / Cahill, K. / Hanigan, M. / Mooers, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133 KB | Display | ![]() |
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PDB format | ![]() | 98.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.6 KB | Display | ![]() |
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Full document | ![]() | 473.3 KB | Display | |
Data in XML | ![]() | 25.9 KB | Display | |
Data in CIF | ![]() | 38.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4z9oC ![]() 4zbkC ![]() 4zc6C ![]() 4gdxS S: Starting model for refinement C: citing same article ( |
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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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Components on special symmetry positions |
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Components
-Gamma-glutamyltranspeptidase 1 ... , 2 types, 2 molecules AB
#1: Protein | Mass: 38533.664 Da / Num. of mol.: 1 / Fragment: Large subunit RESIDUES 28-380 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P19440, gamma-glutamyltransferase, glutathione gamma-glutamate hydrolase, leukotriene-C4 hydrolase |
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#2: Protein | Mass: 20014.438 Da / Num. of mol.: 1 / Fragment: Small subunit RESIDUES 381-569 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P19440, gamma-glutamyltransferase, glutathione gamma-glutamate hydrolase, leukotriene-C4 hydrolase |
-Sugars , 1 types, 6 molecules ![](data/chem/img/NAG.gif)
#3: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 432 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GLU.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GLU.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-GLU / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.99 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG3350, NH4Cl / PH range: 6.0-6.3 / Temp details: Room Temperature |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 15, 2013 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 doble crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50 Å / Num. obs: 37862 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Biso Wilson estimate: 23.09 Å2 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.029 / Rrim(I) all: 0.1 / Χ2: 1.048 / Net I/av σ(I): 21.923 / Net I/σ(I): 9.6 / Num. measured all: 391920 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4GDX Resolution: 2.22→40.02 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.303 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.16 / 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 max: 121.42 Å2 / Biso mean: 35.053 Å2 / Biso min: 17.7 Å2
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Refinement step | Cycle: final / Resolution: 2.22→40.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.22→2.278 Å / Total num. of bins used: 20
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