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Yorodumi- PDB-6xpb: Structure of human GGT1 in complex with 2-amino-4-(((1-((carboxym... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xpb | |||||||||
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Title | Structure of human GGT1 in complex with 2-amino-4-(((1-((carboxymethyl)amino)-1-oxobutan-2-yl)oxy)(phenoxy)phosphoryl)butanoic acid (ACPB) molecule | |||||||||
Components | (Glutathione hydrolase 1 ...) x 2 | |||||||||
Keywords | HYDROLASE / Inhibitor-ENZYME COMPLEX / NTN-HYDROLASE FAMILY / GLYCOPROTEIN / N-GLYCOSYLATION / CELL SURFACE | |||||||||
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: 1.74 Å | |||||||||
Authors | Terzyan, S.S. / Hanigan, M.H. | |||||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Crystal structures of glutathione- and inhibitor-bound human GGT1: critical interactions within the cysteinylglycine binding site. Authors: Terzyan, S.S. / Nguyen, L.T. / Burgett, A.W.G. / Heroux, A. / Smith, C.A. / You, Y. / Hanigan, M.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xpb.cif.gz | 140.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xpb.ent.gz | 104.9 KB | Display | PDB format |
PDBx/mmJSON format | 6xpb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/6xpb ftp://data.pdbj.org/pub/pdb/validation_reports/xp/6xpb | HTTPS FTP |
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-Related structure data
Related structure data | 6xpcC 4gdxS 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
-Glutathione hydrolase 1 ... , 2 types, 2 molecules AB
#1: Protein | Mass: 38533.664 Da / Num. of mol.: 1 / Mutation: V272A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GGT1, GGT / Plasmid: PPICZAA / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 References: UniProt: P19440, glutathione gamma-glutamate hydrolase, gamma-glutamyltransferase, leukotriene-C4 hydrolase |
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#2: Protein | Mass: 20014.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GGT1, GGT / Plasmid: PPICZAA / Production host: Komagataella pastoris (fungus) References: UniProt: P19440, glutathione gamma-glutamate hydrolase, gamma-glutamyltransferase, leukotriene-C4 hydrolase |
-Sugars , 1 types, 6 molecules
#3: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 648 molecules
#4: Chemical | #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-V7D / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20-25% PEG3350, 0.1M ammonium chloride, 0.1M sodium cacodilate pH6.0 Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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 16, 2014 / Details: mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→64 Å / Num. obs: 69800 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.74→1.77 Å / Redundancy: 5 % / Rmerge(I) obs: 0.64 / Num. unique obs: 3284 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4GDX Resolution: 1.74→47.37 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.995 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.093 / 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: 81.88 Å2 / Biso mean: 24.432 Å2 / Biso min: 10.91 Å2
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Refinement step | Cycle: final / Resolution: 1.74→47.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.783 Å / Rfactor Rfree error: 0
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