+Open data
-Basic information
Entry | Database: PDB / ID: 4zbk | ||||||
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Title | Crystal Structure of human GGT1 in complex with GGsTop inhibitor | ||||||
Components | (Gamma-glutamyltranspeptidase ...) x 2 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / ENZYME INHIBITOR COMPLEX / NTN-HYDROLASE FAMILY / N- GLYCOSYLATION / CELL SURFACE / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 / glutamate metabolic process / leukotriene metabolic process / Aflatoxin activation and detoxification / cysteine biosynthetic process / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of immune system process / Paracetamol ADME / zymogen activation / amino acid metabolic process / fatty acid metabolic process / regulation of inflammatory response / spermatogenesis / proteolysis / extracellular space / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.18 Å | ||||||
Model details | Complex | ||||||
Authors | Terzyan, S. / Hanigan, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2015 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: Journal: J.Biol. Chem / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zbk.cif.gz | 132.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zbk.ent.gz | 97.8 KB | Display | PDB format |
PDBx/mmJSON format | 4zbk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/4zbk ftp://data.pdbj.org/pub/pdb/validation_reports/zb/4zbk | HTTPS FTP |
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-Related structure data
Related structure data | 4z9oSC 4zc6C 4zcgC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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
-Gamma-glutamyltranspeptidase ... , 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.) Homo sapiens (human) / Gene: GGT1, GGT / Plasmid: pPICZaA / Production host: PICHIA (fungus) / Strain (production host): X-33 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.) Homo sapiens (human) / Gene: GGT1, GGT / Plasmid: pPICZaA / Production host: PICHIA (fungus) / Strain (production host): X-33 References: UniProt: P19440, gamma-glutamyltransferase, glutathione gamma-glutamate hydrolase, leukotriene-C4 hydrolase |
-Sugars , 1 types, 6 molecules
#3: Sugar | ChemComp-NAG / |
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-Non-polymers , 5 types, 343 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-NA / | #7: Chemical | ChemComp-4M8 / ( | #8: Water | ChemComp-HOH / | |
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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: 2.93 Å3/Da / Density % sol: 58.06 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3 / 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: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2013 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.18→50 Å / Num. obs: 34573 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 32.08 Å2 / Rmerge(I) obs: 0.076 / Χ2: 1.16 / Net I/av σ(I): 24 / Net I/σ(I): 9 / Num. measured all: 201101 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4Z9O Resolution: 2.18→47.13 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.527 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: 113.22 Å2 / Biso mean: 40.918 Å2 / Biso min: 21.07 Å2
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Refinement step | Cycle: final / Resolution: 2.18→47.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.18→2.238 Å
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