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- PDB-7lbc: Structure of human GGT1 in complex with Lnt2-65 compound -

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Basic information

Entry
Database: PDB / ID: 7lbc
TitleStructure of human GGT1 in complex with Lnt2-65 compound
Components(Glutathione hydrolase 1 ...) x 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / substrate-enzyme complex / NTN-hydrolase family / glycoprotein / N-glycosylation / cell surface / 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 / leukotriene metabolic process / glutamate metabolic process / glutathione biosynthetic 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
Chem-XSA / Glutathione hydrolase 1 proenzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.28 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 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 18, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)60,01111
Polymers58,5482
Non-polymers1,4639
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14500 Å2
ΔGint-97 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.216, 122.681, 102.507
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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, 5 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.: 5 / 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 , 4 types, 109 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-XSA / (2R)-2-[(2-aminoethyl)amino]-4-boronobutanoic acid


Mass: 190.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15BN2O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.89 Å3/Da / Density % sol: 57.44 % / Description: transparent rectangular prism
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 22% PEG 3350, 0.1M ammonium chloride, 0.1M sodium cacodylate
Temp details: ROOM TEMPERATURE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 0.92009 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 23, 2019 / Details: Mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92009 Å / Relative weight: 1
ReflectionResolution: 2.28→79.87 Å / Num. obs: 30603 / % possible obs: 99.6 % / Redundancy: 10.1 % / Biso Wilson estimate: 35.9 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.149 / Net I/σ(I): 10.2
Reflection shellResolution: 2.28→2.34 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4259 / CC1/2: 0.911 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
pointlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4Z9O

4z9o


Resolution: 2.28→79.87 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.911 / SU B: 12.894 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.346 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3057 1557 5.1 %RANDOM
Rwork0.2494 ---
obs0.2522 28908 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.79 Å2 / Biso mean: 47.437 Å2 / Biso min: 14.12 Å2
Baniso -1Baniso -2Baniso -3
1-5.01 Å2-0 Å20 Å2
2--0.05 Å20 Å2
3----5.06 Å2
Refinement stepCycle: final / Resolution: 2.28→79.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4026 0 90 105 4221
Biso mean--70.04 40.1 -
Num. residues----529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194227
X-RAY DIFFRACTIONr_angle_refined_deg1.251.9765749
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0465534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25923.626182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.09915664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.111532
X-RAY DIFFRACTIONr_chiral_restr0.0820.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213212
LS refinement shellResolution: 2.28→2.34 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 102 -
Rwork0.414 2044 -
all-2146 -
obs--96.1 %

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