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- PDB-8fdy: Human GAR transformylase in complex with GAR substrate and AGF132... -

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Basic information

Entry
Database: PDB / ID: 8fdy
TitleHuman GAR transformylase in complex with GAR substrate and AGF132 inhibitor
ComponentsPhosphoribosylglycinamide formyltransferase
KeywordsTRANSFERASE / GARFTas / purine biosynthesis / monomer
Function / homology
Function and homology information


phosphoribosylamine-glycine ligase / phosphoribosylglycinamide formyltransferase 1 / adenine biosynthetic process / phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / purine ribonucleoside monophosphate biosynthetic process / phosphoribosylglycinamide formyltransferase activity / phosphoribosylamine-glycine ligase activity / brainstem development / 'de novo' XMP biosynthetic process ...phosphoribosylamine-glycine ligase / phosphoribosylglycinamide formyltransferase 1 / adenine biosynthetic process / phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / purine ribonucleoside monophosphate biosynthetic process / phosphoribosylglycinamide formyltransferase activity / phosphoribosylamine-glycine ligase activity / brainstem development / 'de novo' XMP biosynthetic process / 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
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 / 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 / Phosphoribosylformylglycinamidine cyclo-ligase / Phosphoribosylglycinamide formyltransferase, active site / Phosphoribosylglycinamide formyltransferase active site. / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / 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-XSI / Trifunctional purine biosynthetic protein adenosine-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsWong-Roushar, J. / Dann III, C.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA166711 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA250469 United States
CitationJournal: Acs Pharmacol Transl Sci / Year: 2023
Title: Multitargeted 6-Substituted Thieno[2,3- d ]pyrimidines as Folate Receptor-Selective Anticancer Agents that Inhibit Cytosolic and Mitochondrial One-Carbon Metabolism.
Authors: Tong, N. / Wong-Roushar, J. / Wallace-Povirk, A. / Shah, Y. / Nyman, M.C. / Katinas, J.M. / Schneider, M. / O'Connor, C. / Bao, X. / Kim, S. / Li, J. / Hou, Z. / Matherly, L.H. / Dann 3rd, C.E. / Gangjee, A.
History
DepositionDec 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoribosylglycinamide formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5683
Polymers22,8101
Non-polymers7582
Water1,08160
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)74.659, 74.659, 100.793
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 Phosphoribosylglycinamide formyltransferase


Mass: 22810.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GART, PGFT, PRGS
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P22102, phosphoribosylglycinamide formyltransferase 1
#2: Chemical ChemComp-GAR / GLYCINAMIDE RIBONUCLEOTIDE


Mass: 284.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13N2O8P
#3: Chemical ChemComp-XSI / N-{5-[4-(2-amino-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidin-6-yl)butyl]pyridine-2-carbonyl}-L-glutamic acid


Mass: 473.502 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23N5O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 3.56 Å3/Da / Density % sol: 65.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Tris-HCl pH 7.5, 0.33 M NaCl, 16-21% 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: Dec 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.06→39.7558 Å / Num. obs: 20659 / % possible obs: 100 % / Redundancy: 10.5 % / CC1/2: 0.997 / Rpim(I) all: 0.064 / Rrim(I) all: 0.209 / Net I/σ(I): 11
Reflection shellResolution: 2.06→2.12 Å / Num. unique obs: 1578 / CC1/2: 0.383

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Processing

Software
NameVersionClassification
PHENIX1.13-2998refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J9F

5j9f


Resolution: 2.06→39.7558 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 960 4.67 %
Rwork0.2106 --
obs0.2128 20576 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→39.7558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1487 0 51 60 1598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051572
X-RAY DIFFRACTIONf_angle_d0.8632141
X-RAY DIFFRACTIONf_dihedral_angle_d16.756934
X-RAY DIFFRACTIONf_chiral_restr0.051256
X-RAY DIFFRACTIONf_plane_restr0.003273
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.16860.32341290.30152732X-RAY DIFFRACTION99
2.1686-2.30450.30941320.26822757X-RAY DIFFRACTION100
2.3045-2.48240.25621250.23922771X-RAY DIFFRACTION100
2.4824-2.73220.26981370.23462802X-RAY DIFFRACTION100
2.7322-3.12740.26981150.21442814X-RAY DIFFRACTION100
3.1274-3.93960.2871470.19062820X-RAY DIFFRACTION100
3.9396-39.75580.21161750.18642920X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -31.8136 Å / Origin y: 18.8203 Å / Origin z: 27.9284 Å
111213212223313233
T0.2736 Å2-0.0031 Å2-0.0092 Å2-0.2028 Å20.0168 Å2--0.2863 Å2
L1.9796 °20.7415 °21.4964 °2-1.3658 °20.8614 °2--2.4322 °2
S0.1314 Å °-0.0564 Å °-0.4063 Å °0.079 Å °0.061 Å °-0.0202 Å °0.3407 Å °0.0043 Å °-0.1128 Å °
Refinement TLS groupSelection details: all

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