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- PDB-6dz0: Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosph... -

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Basic information

Entry
Database: PDB / ID: 6dz0
TitleCrystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with (3R,4S)-1-((4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl)-4-((pent-4-yn-1-ylthio)methyl)pyrrolidin-3-ol
ComponentsS-methyl-5'-thioadenosine phosphorylase
KeywordsTRANSFERASE / MTAP enzyme / cancer / phosphorylase
Function / homology
Function and homology information


Methionine salvage pathway / 1,4-alpha-oligoglucan phosphorylase activity / S-methyl-5'-thioadenosine phosphorylase / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / response to testosterone / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / methylation ...Methionine salvage pathway / 1,4-alpha-oligoglucan phosphorylase activity / S-methyl-5'-thioadenosine phosphorylase / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / response to testosterone / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / methylation / extracellular exosome / nucleoplasm / cytosol
Similarity search - Function
Methylthioadenosine phosphorylase (MTAP) / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-OS3 / PHOSPHATE ION / S-methyl-5'-thioadenosine phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsHarijan, R.K. / Ducati, R.G. / Bonanno, J.B. / Almo, S.C. / Schramm, V.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: J. Med. Chem. / Year: 2019
Title: Selective Inhibitors of Helicobacter pylori Methylthioadenosine Nucleosidase and Human Methylthioadenosine Phosphorylase.
Authors: Harijan, R.K. / Hoff, O. / Ducati, R.G. / Firestone, R.S. / Hirsch, B.M. / Evans, G.B. / Schramm, V.L. / Tyler, P.C.
History
DepositionJul 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Apr 24, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-methyl-5'-thioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9059
Polymers33,1191
Non-polymers7868
Water4,432246
1
A: S-methyl-5'-thioadenosine phosphorylase
hetero molecules

A: S-methyl-5'-thioadenosine phosphorylase
hetero molecules

A: S-methyl-5'-thioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,71627
Polymers99,3573
Non-polymers2,35924
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
Buried area9930 Å2
ΔGint-55 kcal/mol
Surface area30250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.812, 121.812, 44.372
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-308-

CL

21A-499-

HOH

31A-606-

HOH

41A-609-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein S-methyl-5'-thioadenosine phosphorylase / 5'-methylthioadenosine phosphorylase / MTAPase


Mass: 33119.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTAP, MSAP / Production host: Escherichia coli (E. coli)
References: UniProt: Q13126, S-methyl-5'-thioadenosine phosphorylase

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Non-polymers , 5 types, 254 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-OS3 / (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(pent-4-yn-1-yl)sulfanyl]methyl}pyrrolidin-3-ol


Mass: 345.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H23N5OS
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

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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: 2.9 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100 mM HEPES, pH 7.0, 10% w/v PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 14, 2017 / Details: KB mirrors
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.62→105.49 Å / Num. obs: 48221 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.999 / Net I/σ(I): 2
Reflection shellResolution: 1.62→1.65 Å / Num. measured obs: 27711 / CC1/2: 0.714

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5TC6

5tc6


Resolution: 1.62→105.49 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.353 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.067 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17569 2484 5.2 %RANDOM
Rwork0.15533 ---
obs0.15641 45734 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.645 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.62→105.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2113 0 50 246 2409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192221
X-RAY DIFFRACTIONr_bond_other_d0.0020.022108
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.9753002
X-RAY DIFFRACTIONr_angle_other_deg0.96934902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1995281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81924.0786
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.55415392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8811513
X-RAY DIFFRACTIONr_chiral_restr0.0840.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022402
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02421
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_it1.4962.0321105
X-RAY DIFFRACTIONr_mcbond_other1.4952.031104
X-RAY DIFFRACTIONr_mcangle_it2.43.041384
X-RAY DIFFRACTIONr_mcangle_other2.43.0431385
X-RAY DIFFRACTIONr_scbond_it2.452.3621115
X-RAY DIFFRACTIONr_scbond_other2.4492.3631116
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8143.4011616
X-RAY DIFFRACTIONr_long_range_B_refined6.31926.1662537
X-RAY DIFFRACTIONr_long_range_B_other6.31826.1712538
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 162 -
Rwork0.233 3356 -
obs--99.94 %

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