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- PDB-7ld9: Structure of human GGT1 in complex with ABBA -

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Basic information

Entry
Database: PDB / ID: 7ld9
TitleStructure of human GGT1 in complex with ABBA
Components(Glutathione hydrolase 1 ...) x 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / substrate-enzyme complex / NTN-hydrolase family / glycoprotein / N-glycosylation / cell surface / HYDROLASE-HYDROLASE INHIBITOR complex / ABBA
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 / 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
Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase signature. / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase, large subunit, C-terminal domain / Gamma-glutamyltranspeptidase, small subunit / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
(2S)-2-amino-4-boronobutanoic acid / (2R)-2-amino-4-boronobutanoic acid / Glutathione hydrolase 1 proenzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.42 Å
AuthorsTerzyan, S.S. / Hanigan, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM125952 United States
CitationJournal: Bioorg.Med.Chem. / Year: 2022
Title: Design and evaluation of novel analogs of 2-amino-4-boronobutanoic acid (ABBA) as inhibitors of human gamma-glutamyl transpeptidase.
Authors: Nguyen, L. / Schultz, D.C. / Terzyan, S.S. / Rezaei, M. / Songb, J. / Li, C. / You, Y. / Hanigan, M.H.
History
DepositionJan 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione hydrolase 1 heavy chain
B: Glutathione hydrolase 1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,97816
Polymers58,5482
Non-polymers2,43014
Water13,241735
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15760 Å2
ΔGint-79 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.319, 125.570, 104.388
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-962-

HOH

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Components

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Glutathione hydrolase 1 ... , 2 types, 2 molecules AB

#1: Protein Glutathione hydrolase 1 heavy chain / GGT 1 / Gamma-glutamyltransferase 1 / Glutathione hydrolase 1 / Leukotriene-C4 hydrolase


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
#2: Protein Glutathione hydrolase 1 light chain / GGT 1 / Gamma-glutamyltransferase 1 / Glutathione hydrolase 1 / Leukotriene-C4 hydrolase


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) / Strain (production host): X-33
References: UniProt: P19440, glutathione gamma-glutamate hydrolase, gamma-glutamyltransferase, leukotriene-C4 hydrolase

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Sugars , 1 types, 6 molecules

#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 743 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Chemical ChemComp-XUJ / (2R)-2-amino-4-boronobutanoic acid


Mass: 146.937 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10BNO4
#8: Chemical ChemComp-XU7 / (2S)-2-amino-4-boronobutanoic acid


Mass: 146.937 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10BNO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.06 % / Description: transparent rectangular prism
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20-25%PEG3350, 0.1M ammonium cloride, 0.1M sodium cacodilate pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 21, 2017 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.42→81 Å / Num. obs: 128369 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 25.57
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.714 / Mean I/σ(I) obs: 2.44 / Num. unique obs: 5352 / % possible all: 83.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0073phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4Z9O

4z9o


Resolution: 1.42→80.69 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.455 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.134 6480 5 %RANDOM
Rwork0.107 ---
obs0.108 121859 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.42→80.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4048 0 152 735 4935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194521
X-RAY DIFFRACTIONr_bond_other_d0.0050.024317
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.9866185
X-RAY DIFFRACTIONr_angle_other_deg1.1713.0099904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9035586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95423.333192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35415712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3731537
X-RAY DIFFRACTIONr_chiral_restr0.1530.2706
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215237
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021046
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.83838836
X-RAY DIFFRACTIONr_sphericity_free44.1695181
X-RAY DIFFRACTIONr_sphericity_bonded12.94859279
LS refinement shellResolution: 1.42→1.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 471 -
Rwork0.218 8741 -
obs--97.12 %

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