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- PDB-8fjx: Human GAR transformylase in complex with GAR substrate and AGF320... -

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Basic information

Entry
Database: PDB / ID: 8fjx
TitleHuman GAR transformylase in complex with GAR substrate and AGF320 inhibitor
ComponentsTrifunctional purine biosynthetic protein adenosine-3
KeywordsLIGASE/INHIBITOR / GARFTase / purine biosynthesis / monomer / inhibitor / LIGASE / LIGASE-INHIBITOR complex
Function / homology
Function and homology information


adenine biosynthetic process / phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / phosphoribosylamine-glycine ligase / phosphoribosylglycinamide formyltransferase 1 / phosphoribosylamine-glycine ligase activity / purine ribonucleoside monophosphate biosynthetic process / phosphoribosylglycinamide formyltransferase activity / 'de novo' XMP biosynthetic process / brainstem development ...adenine biosynthetic process / phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / phosphoribosylamine-glycine ligase / phosphoribosylglycinamide formyltransferase 1 / phosphoribosylamine-glycine ligase activity / purine ribonucleoside monophosphate biosynthetic process / phosphoribosylglycinamide formyltransferase activity / 'de novo' XMP biosynthetic process / brainstem development / Purine ribonucleoside monophosphate biosynthesis / 'de novo' AMP biosynthetic process / purine nucleotide biosynthetic process / GMP biosynthetic process / 'de novo' IMP biosynthetic process / cerebellum development / cerebral cortex development / extracellular exosome / ATP binding / metal ion binding / cytosol
Similarity search - Function
Phosphoribosylformylglycinamidine cyclo-ligase / Phosphoribosylglycinamide synthetase / Phosphoribosylglycinamide synthetase, conserved site / Phosphoribosylglycinamide synthetase, C-domain / Phosphoribosylglycinamide synthetase, N-terminal / Phosphoribosylglycinamide synthetase, C-domain superfamily / Phosphoribosylglycinamide synthetase, C domain / Phosphoribosylglycinamide synthetase, N domain / Phosphoribosylglycinamide synthetase signature. / Phosphoribosylglycinamide synthetase, C domain ...Phosphoribosylformylglycinamidine cyclo-ligase / Phosphoribosylglycinamide synthetase / Phosphoribosylglycinamide synthetase, conserved site / Phosphoribosylglycinamide synthetase, C-domain / Phosphoribosylglycinamide synthetase, N-terminal / Phosphoribosylglycinamide synthetase, C-domain superfamily / Phosphoribosylglycinamide synthetase, C domain / Phosphoribosylglycinamide synthetase, N domain / Phosphoribosylglycinamide synthetase signature. / Phosphoribosylglycinamide synthetase, C domain / Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / Phosphoribosylglycinamide formyltransferase / Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / Phosphoribosylglycinamide formyltransferase, active site / Phosphoribosylglycinamide formyltransferase active site. / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Rudiment single hybrid motif / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile.
Similarity search - Domain/homology
GLYCINAMIDE RIBONUCLEOTIDE / Chem-Y7L / Trifunctional purine biosynthetic protein adenosine-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsWong-Roushar, J. / Dann III, C.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA250469 United States
CitationJournal: J.Med.Chem. / Year: 2023
Title: Structure-Based Design of Transport-Specific Multitargeted One-Carbon Metabolism Inhibitors in Cytosol and Mitochondria.
Authors: Nayeen, M.J. / Katinas, J.M. / Magdum, T. / Shah, K. / Wong, J.E. / O'Connor, C.E. / Fifer, A.N. / Wallace-Povirk, A. / Hou, Z. / Matherly, L.H. / Dann 3rd, C.E. / Gangjee, A.
History
DepositionDec 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trifunctional purine biosynthetic protein adenosine-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5703
Polymers22,8101
Non-polymers7602
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.251, 75.251, 100.037
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Trifunctional purine biosynthetic protein adenosine-3


Mass: 22810.139 Da / Num. of mol.: 1 / Fragment: UNP residues 808-1010
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GART, PGFT, PRGS / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P22102, phosphoribosylamine-glycine ligase, phosphoribosylformylglycinamidine cyclo-ligase, phosphoribosylglycinamide formyltransferase 1
#2: Chemical ChemComp-Y7L / N-{5-[5-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)pentyl]thiophene-2-carbonyl}-L-glutamic acid


Mass: 475.518 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H25N5O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GAR / GLYCINAMIDE RIBONUCLEOTIDE


Mass: 284.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13N2O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
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: 3.58 Å3/Da / Density % sol: 65.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Tris (pH 7.5), 0.333 mM NaCl, 20% polyethylene glycol (PEG) 4000, and 2% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jun 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→39.6853 Å / Num. obs: 17854 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.997 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.062 / Rrim(I) all: 0.196 / Net I/σ(I): 11.6
Reflection shellResolution: 2.17→2.24 Å / Rmerge(I) obs: 3.414 / Num. unique obs: 1501 / CC1/2: 0.437 / Rpim(I) all: 1.344 / Rrim(I) all: 3.68

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Processing

Software
NameVersionClassification
PHENIX1.13-2998refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→39.6853 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2458 856 5.05 %
Rwork0.2027 --
obs0.2048 16944 95.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.17→39.6853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1503 0 51 76 1630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041601
X-RAY DIFFRACTIONf_angle_d0.7392177
X-RAY DIFFRACTIONf_dihedral_angle_d12.922959
X-RAY DIFFRACTIONf_chiral_restr0.049258
X-RAY DIFFRACTIONf_plane_restr0.003278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1701-2.24770.4092810.43011191X-RAY DIFFRACTION73
2.2477-2.33770.3038730.30991270X-RAY DIFFRACTION77
2.3377-2.4440.3268780.26551688X-RAY DIFFRACTION100
2.444-2.57290.2658660.26031673X-RAY DIFFRACTION100
2.5729-2.7340.27021010.24261670X-RAY DIFFRACTION100
2.734-2.94510.2603850.22971683X-RAY DIFFRACTION100
2.9451-3.24130.2984870.21181692X-RAY DIFFRACTION100
3.2413-3.710.21571120.17761673X-RAY DIFFRACTION100
3.71-4.67310.1837830.15651742X-RAY DIFFRACTION100
3.9423-39.68530.20481490.16182963X-RAY DIFFRACTION100
4.6731-39.68530.2294900.16921806X-RAY DIFFRACTION100

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