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- PDB-5fi7: Crystal structure of human GAC in complex with inhibitor UPGL_000... -

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Basic information

Entry
Database: PDB / ID: 5fi7
TitleCrystal structure of human GAC in complex with inhibitor UPGL_00015: 2-phenyl-~{N}-[5-[(3~{S})-3-[[5-(2-phenylethanoylamino)-1,3,4-thiadiazol-2-yl]oxy]pyrrolidin-1-yl]-1,3,4-thiadiazol-2-yl]ethanamide
ComponentsGlutaminase kidney isoform, mitochondrial
KeywordsHYDROLASE/HYDROLASE INHIBITOR / glutaminase C / complex / inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


glutamine catabolic process / regulation of respiratory gaseous exchange by nervous system process / glutamate biosynthetic process / Glutamate and glutamine metabolism / intracellular glutamate homeostasis / Glutamate Neurotransmitter Release Cycle / glutaminase / glutaminase activity / suckling behavior / TP53 Regulates Metabolic Genes ...glutamine catabolic process / regulation of respiratory gaseous exchange by nervous system process / glutamate biosynthetic process / Glutamate and glutamine metabolism / intracellular glutamate homeostasis / Glutamate Neurotransmitter Release Cycle / glutaminase / glutaminase activity / suckling behavior / TP53 Regulates Metabolic Genes / chemical synaptic transmission / protein homotetramerization / mitochondrial matrix / synapse / mitochondrion / cytosol
Similarity search - Function
Recoverin; domain 1 - #210 / Glutaminase, EF-hand domain / EF-hand domain / Glutaminase / Glutaminase / Recoverin; domain 1 / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. ...Recoverin; domain 1 - #210 / Glutaminase, EF-hand domain / EF-hand domain / Glutaminase / Glutaminase / Recoverin; domain 1 / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Beta-lactamase/transpeptidase-like / Ankyrin repeat-containing domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-5XZ / Glutaminase kidney isoform, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHuang, Q. / Cerione, R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM040654 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM047458 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM061762 United States
CitationJournal: Bioorg.Med.Chem. / Year: 2016
Title: Design and evaluation of novel glutaminase inhibitors.
Authors: McDermott, L.A. / Iyer, P. / Vernetti, L. / Rimer, S. / Sun, J. / Boby, M. / Yang, T. / Fioravanti, M. / O'Neill, J. / Wang, L. / Drakes, D. / Katt, W. / Huang, Q. / Cerione, R.
History
DepositionDec 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutaminase kidney isoform, mitochondrial
B: Glutaminase kidney isoform, mitochondrial
C: Glutaminase kidney isoform, mitochondrial
D: Glutaminase kidney isoform, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,8746
Polymers237,8304
Non-polymers1,0432
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8120 Å2
ΔGint-26 kcal/mol
Surface area62250 Å2
2
A: Glutaminase kidney isoform, mitochondrial
C: Glutaminase kidney isoform, mitochondrial
hetero molecules

B: Glutaminase kidney isoform, mitochondrial
D: Glutaminase kidney isoform, mitochondrial


Theoretical massNumber of molelcules
Total (without water)238,8746
Polymers237,8304
Non-polymers1,0432
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Buried area10330 Å2
ΔGint-42 kcal/mol
Surface area60040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.174, 138.829, 176.653
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Glutaminase kidney isoform, mitochondrial / GLS / K-glutaminase / L-glutamine amidohydrolase


Mass: 59457.590 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: O94925
#2: Chemical ChemComp-5XZ / 2-phenyl-~{N}-[5-[(3~{S})-3-[[5-(2-phenylethanoylamino)-1,3,4-thiadiazol-2-yl]oxy]pyrrolidin-1-yl]-1,3,4-thiadiazol-2-yl]ethanamide


Mass: 521.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H23N7O3S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG6000, LiCl, Tris-HCl / PH range: 8.0-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 107585 / % possible obs: 98.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 14.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D3O

5d3o


Resolution: 2.5→44.904 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2669 1571 1.86 %Random selection
Rwork0.2176 ---
obs0.2185 84511 99.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→44.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12776 0 72 202 13050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813144
X-RAY DIFFRACTIONf_angle_d1.03717740
X-RAY DIFFRACTIONf_dihedral_angle_d15.2987882
X-RAY DIFFRACTIONf_chiral_restr0.0531938
X-RAY DIFFRACTIONf_plane_restr0.0072288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.58070.33411420.27787457X-RAY DIFFRACTION99
2.5807-2.67290.2731420.2727478X-RAY DIFFRACTION100
2.6729-2.77990.40681420.25387425X-RAY DIFFRACTION100
2.7799-2.90640.32581410.24937501X-RAY DIFFRACTION100
2.9064-3.05960.29621430.25437508X-RAY DIFFRACTION100
3.0596-3.25130.34751420.25587483X-RAY DIFFRACTION100
3.2513-3.50220.2861420.23237551X-RAY DIFFRACTION100
3.5022-3.85450.25661440.20487557X-RAY DIFFRACTION100
3.8545-4.41180.22651430.18097588X-RAY DIFFRACTION100
4.4118-5.55680.20781460.18377657X-RAY DIFFRACTION100
5.5568-44.91120.22851440.2017735X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 53.7064 Å / Origin y: -37.3213 Å / Origin z: -31.1633 Å
111213212223313233
T0.2331 Å20.0033 Å2-0.0095 Å2-0.1859 Å20.0128 Å2--0.1619 Å2
L0.1286 °20.0397 °2-0.0068 °2-0.1879 °20.1246 °2--0.1321 °2
S-0.0065 Å °0.0453 Å °-0.0081 Å °-0.0734 Å °0.0307 Å °0.0009 Å °-0.0044 Å °0.0113 Å °0 Å °
Refinement TLS groupSelection details: all

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