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- PDB-3ggj: Human hypoxanthine-guanine phosphoribosyltransferase in complex w... -

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Basic information

Entry
Database: PDB / ID: 3ggj
TitleHuman hypoxanthine-guanine phosphoribosyltransferase in complex with 9-(2-phosphonoethoxyethyl)guanine
ComponentsHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE / purine salvage / anti-malarial chemotherapeutic / acyclic nucleoside phosphonate / Disease mutation / Glycosyltransferase / Gout / Magnesium / Metal-binding
Function / homology
Function and homology information


adenine metabolic process / Defective HPRT1 disrupts guanine and hypoxanthine salvage / GMP catabolic process / guanine salvage / hypoxanthine salvage / hypoxanthine metabolic process / cerebral cortex neuron differentiation / positive regulation of dopamine metabolic process / hypoxanthine phosphoribosyltransferase / lymphocyte proliferation ...adenine metabolic process / Defective HPRT1 disrupts guanine and hypoxanthine salvage / GMP catabolic process / guanine salvage / hypoxanthine salvage / hypoxanthine metabolic process / cerebral cortex neuron differentiation / positive regulation of dopamine metabolic process / hypoxanthine phosphoribosyltransferase / lymphocyte proliferation / guanine phosphoribosyltransferase activity / IMP metabolic process / GMP salvage / hypoxanthine phosphoribosyltransferase activity / grooming behavior / Purine salvage / IMP salvage / striatum development / AMP salvage / dopaminergic neuron differentiation / purine nucleotide biosynthetic process / purine ribonucleoside salvage / Azathioprine ADME / dendrite morphogenesis / central nervous system neuron development / dopamine metabolic process / response to amphetamine / locomotory behavior / T cell mediated cytotoxicity / protein homotetramerization / nucleotide binding / magnesium ion binding / extracellular exosome / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Hypoxanthine phosphoribosyl transferase / : / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-25H / Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsGuddat, L.W. / Keough, D.T. / Jersey, J.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Inhibition of hypoxanthine-guanine phosphoribosyltransferase by acyclic nucleoside phosphonates: a new class of antimalarial therapeutics.
Authors: Keough, D.T. / Hockova, D. / Holy, A. / Naesens, L.M. / Skinner-Adams, T.S. / Jersey, J. / Guddat, L.W.
History
DepositionFeb 28, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypoxanthine-guanine phosphoribosyltransferase
B: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5694
Polymers48,9622
Non-polymers6062
Water1,982110
1
A: Hypoxanthine-guanine phosphoribosyltransferase
B: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules

A: Hypoxanthine-guanine phosphoribosyltransferase
B: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,1388
Polymers97,9254
Non-polymers1,2134
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area9560 Å2
ΔGint-31 kcal/mol
Surface area34760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.189, 72.754, 51.387
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-274-

HOH

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Components

#1: Protein Hypoxanthine-guanine phosphoribosyltransferase / HGPRTase / HGPRT


Mass: 24481.217 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPRT, HPRT1, HPT / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): sphi606
References: UniProt: P00492, hypoxanthine phosphoribosyltransferase
#2: Chemical ChemComp-25H / {2-[2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)ethoxy]ethyl}phosphonic acid / 9-(2-phosphonoethoxyethyl)guanine


Mass: 303.212 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N5O5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.12 Å3/Da / Density % sol: 42.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M citrate, 10% iso-propanol, 29% PEG 4000, 3.3mM inhibitor , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 6, 2007 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→27.78 Å / Num. all: 13454 / Num. obs: 13236 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 6.8
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1320 / Rsym value: 0.3 / % possible all: 99.2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
REFMAC5.5.0066refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3GEP

3gep


Resolution: 2.6→27.78 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.865 / SU B: 30.992 / SU ML: 0.318 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.411 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29521 657 5 %RANDOM
Rwork0.2363 ---
obs0.2393 12574 98.72 %-
all-13236 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.386 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.6→27.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3289 0 40 110 3439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223402
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.9944611
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0225423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.41623.889144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.04315581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.11521
X-RAY DIFFRACTIONr_chiral_restr0.0830.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212535
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9731.52113
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7623403
X-RAY DIFFRACTIONr_scbond_it1.19631289
X-RAY DIFFRACTIONr_scangle_it2.0954.51206
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 52 -
Rwork0.275 895 -
obs--98.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.66570.0519-0.25360.9642-0.17260.4733-0.08460.03350.14160.07940.02460.03030.102-0.02370.06010.1160.02180.01640.14240.02960.128310.24746.163717.079
21.84640.3194-2.22786.1922-1.18487.9117-0.09740.03170.2714-0.50970.06720.17610.14-0.23430.03030.0513-0.0033-0.05360.0085-0.01480.177110.515266.5317.5438
30.08570.14680.04771.82840.74041.6265-0.0740.01910.109-0.10830.0342-0.2017-0.019-0.02280.03980.09040.0073-0.04470.13240.04330.274817.358454.921612.8509
40.2824-0.46610.4071.706-0.34970.91670.0811-0.0003-0.0627-0.3049-0.01510.079-0.0890.0936-0.0660.17480.00170.0010.15740.00890.11829.272825.499610.2346
50.1077-0.3330.04542.9115-0.03970.099-0.002-0.056-0.0942-0.4641-0.00010.32630.0945-0.05580.00210.2819-0.0018-0.03670.0533-0.00770.34678.72844.682310.4721
60.2207-0.18310.37992.02140.19822.24180.1001-0.0233-0.0715-0.21160.0623-0.16320.17260.1338-0.16250.11490.0250.00130.10070.00890.161815.072716.37314.313
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 100
2X-RAY DIFFRACTION2A101 - 130
3X-RAY DIFFRACTION3A131 - 217
4X-RAY DIFFRACTION4B4 - 100
5X-RAY DIFFRACTION5B101 - 130
6X-RAY DIFFRACTION6B131 - 217

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