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- PDB-4ijq: Human hypoxanthine-guanine phosphoribosyltransferase in complex w... -

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Basic information

Entry
Database: PDB / ID: 4ijq
TitleHuman hypoxanthine-guanine phosphoribosyltransferase in complex with [(2-((Guanine-9H-yl)methyl)propane-1,3-diyl)bis(oxy)]bis(methylene))diphosphonic acid
ComponentsHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE / GMP
Function / homology
Function and homology information


Defective HPRT1 disrupts guanine and hypoxanthine salvage / positive regulation of dopamine metabolic process / adenine metabolic process / GMP catabolic process / sperm annulus / cerebral cortex neuron differentiation / hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / guanine salvage / lymphocyte proliferation ...Defective HPRT1 disrupts guanine and hypoxanthine salvage / positive regulation of dopamine metabolic process / adenine metabolic process / GMP catabolic process / sperm annulus / cerebral cortex neuron differentiation / hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / guanine salvage / lymphocyte proliferation / hypoxanthine metabolic process / hypoxanthine salvage / IMP metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / Purine salvage / IMP salvage / grooming behavior / AMP salvage / striatum development / dopaminergic neuron differentiation / purine nucleotide biosynthetic process / purine ribonucleoside salvage / Azathioprine ADME / dendrite morphogenesis / central nervous system neuron development / dopamine metabolic process / T cell mediated cytotoxicity / response to amphetamine / sperm end piece / locomotory behavior / sperm principal piece / sperm midpiece / protein homotetramerization / nucleotide binding / magnesium ion binding / extracellular exosome / identical protein binding / cytoplasm / cytosol
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-SV2 / Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.004 Å
AuthorsGuddat, L.W. / Keough, D.T. / Hockova, D.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Acyclic nucleoside phosphonates containing a second phosphonate group are potent inhibitors of 6-oxopurine phosphoribosyltransferases and have antimalarial activity
Authors: Keough, D.T. / Spacek, P. / Hockova, D. / Tichy, T. / Vrbkova, S. / Slavetinska, L. / Janeba, Z. / Naesens, L. / Edstein, M.D. / Chavchich, M. / Wang, T.H. / Jersey, J. / Guddat, L.W.
History
DepositionDec 22, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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
C: Hypoxanthine-guanine phosphoribosyltransferase
D: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,52820
Polymers101,2404
Non-polymers2,28816
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12780 Å2
ΔGint-180 kcal/mol
Surface area29690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.505, 127.741, 64.756
Angle α, β, γ (deg.)90.00, 102.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 25310.102 Da / Num. of mol.: 4 / Fragment: human HGPRT, UNP residues 4-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPRT1, HPRT / Production host: Escherichia coli (E. coli)
References: UniProt: P00492, hypoxanthine phosphoribosyltransferase
#2: Chemical
ChemComp-SV2 / [{2-[(guanine-9-yl)methyl]propane-1,3-diyl}bis(oxymethylene)]bis(phosphonic acid)


Mass: 427.244 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H19N5O9P2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.26 Å3/Da / Density % sol: 45.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M LiSO4, 30% PEG5000MME, 0.1M Tris-HCl, 0.88mM ligand, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 9, 2011
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2→19.87 Å / Num. all: 59187 / Num. obs: 59187 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.102 / Rsym value: 0.102

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.004→19.867 Å / SU ML: 0.24 / σ(F): 0.01 / Phase error: 22.27 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 2000 3.53 %Random
Rwork0.1734 ---
obs0.1751 56605 94.12 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.19 Å2 / ksol: 0.374 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0634 Å2-0 Å2-2.4428 Å2
2---3.9473 Å2-0 Å2
3---0.923 Å2
Refinement stepCycle: LAST / Resolution: 2.004→19.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6401 0 136 284 6821
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146698
X-RAY DIFFRACTIONf_angle_d1.2879121
X-RAY DIFFRACTIONf_dihedral_angle_d16.5742506
X-RAY DIFFRACTIONf_chiral_restr0.091007
X-RAY DIFFRACTIONf_plane_restr0.0051132
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.004-2.07510.2871650.2588452279
2.0751-2.15810.27451920.2085523390
2.1581-2.25620.27431990.1931541994
2.2562-2.3750.25842000.1948546094
2.375-2.52350.25172020.1832553696
2.5235-2.71790.24452070.1827564297
2.7179-2.99060.23842080.1877568098
2.9906-3.42140.23982090.1715570198
3.4214-4.30340.16462100.1454572898
4.3034-19.8680.19952080.1569568497
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)
13.58771.6207-1.07462.1132-0.24184.62460.08360.32120.4819-0.2380.03620.5676-0.1933-0.5804-0.16760.20470.0602-0.08910.1581-0.00340.3267-19.1098-31.2145-25.9047
21.834-1.71730.85194.08861.57023.407-0.03110.004-0.0123-0.03050.018-0.2148-0.05670.2670.04340.1292-0.03830.00510.17570.03980.1963.0245-35.8871-21.3097
35.53671.4830.1573.1499-2.46022.25360.10420.06170.30920.0638-0.2349-0.202-0.01640.1109-0.02750.0919-0.0493-0.06790.16430.01120.18269.9796-30.4737-13.4501
43.57610.25741.24373.0857-0.09462.9120.0494-0.0608-0.3025-0.038-0.0603-0.2939-0.20980.27890.02650.1253-0.06010.01290.10750.04660.15813.7793-20.522-22.3255
54.5279-0.3303-1.63221.35420.39344.3872-0.0333-0.15220.29340.045-0.27560.6472-0.4186-0.329-0.04790.10840.0543-0.0450.1102-0.04370.3003-16.6114-24.9068-18.186
65.1175-1.7221.37692.56010.55081.3853-0.2420.59261.0246-0.1436-0.07050.1872-0.34880.01180.17370.44970.0413-0.13150.20470.06790.3411-17.8248-37.2645-39.0272
74.221-0.2964-0.01137.11452.98423.3064-0.12750.50690.3417-0.68230.4394-0.3787-0.24680.1557-0.24640.277-0.01590.00750.21760.05720.2157-2.7813-42.7784-39.8161
86.62285.1466-4.16367.2944-4.19576.69310.3536-0.58630.04970.3063-0.13490.7401-0.4421-0.3585-0.1090.14870.0264-0.04660.14990.00780.2919-21.8683-47.1732-23.9711
95.126-1.3378-1.93174.39411.49882.4110.2315-0.5629-0.19560.1944-0.06111.0563-0.2102-0.18320.39510.15890.01010.03180.2270.01780.3046-22.5721-61.4445-26.8017
101.0963-1.8767-1.89625.81674.43327.0999-0.0086-0.25680.12720.2566-0.0793-0.0540.19260.45480.13870.1657-0.0224-0.05290.16790.02340.2265-16.517-54.3735-21.9246
113.02580.40881.13373.0378-1.19452.1590.0725-0.2177-0.10440.0385-0.06460.32660.0889-0.1560.01020.1025-0.009-0.0050.0614-0.02290.1244-23.5514-62.9739-29.0735
127.13154.812-4.04415.3959-6.54179.1412-0.12530.4065-0.2312-0.39240.10680.45680.2397-0.43990.05290.29670.0174-0.06190.2164-0.08840.3483-30.7134-64.0988-38.5274
137.5155.4208-2.61348.3316-3.79975.00930.0459-0.15810.19460.18330.0180.7019-0.1742-0.3824-0.10140.14210.0186-0.04610.1228-0.01580.2378-28.3813-56.4801-32.065
142.44180.99691.61912.1891-1.19023.57110.0090.28580.1943-0.35390.41230.3833-0.2059-0.1452-0.28880.2677-0.0015-0.1320.22140.05510.3118-28.2144-49.412-40.5591
156.6567-1.4126-1.82483.02960.73463.21420.10150.5046-0.0948-0.541-0.14020.25930.0275-0.04510.06780.248-0.0014-0.03750.12990.02330.1319-12.9909-50.2435-42.0669
166.3603-1.2224-2.10813.2867-0.65593.5227-0.04840.5792-0.1153-0.96940.0565-0.0428-0.25810.08360.01720.2922-0.05990.00050.17280.0020.1302-5.2656-50.1783-44.7897
172.47331.2578-2.94722.1799-0.79953.8325-0.37740.0341-0.33720.5653-0.0748-0.1661.33490.47620.20340.36940.105-0.06790.31330.02460.26763.8135-57.76020.8178
183.60171.89880.47485.22530.52872.1747-0.0101-0.2845-0.26720.0154-0.0329-0.76280.24540.56090.05810.16470.0492-0.05830.24710.01270.319212.2864-51.8565-10.6829
192.2338-0.62361.02685.5751-0.76060.7605-0.1059-0.1407-0.12040.13560.19080.36580.0289-0.2026-0.07830.16780.00530.03010.2880.00970.0957-10.7891-42.1387-3.2453
208.5935.22446.33186.79072.2075.477-0.48980.13090.3204-0.46140.19810.0386-0.05870.14320.32290.16710.01860.04320.1756-0.00260.149-9.3558-40.3779-9.0968
210.8351-1.3374-0.65042.42370.30162.241-0.0644-0.20590.48290.418-0.0520.41430.2434-0.0769-0.03360.24310.05080.05560.2871-0.03380.2645-13.8112-33.9357-6.0631
221.17030.85510.17423.66540.77342.9616-0.0648-0.247-0.02290.29960.26260.0689-0.564-0.2096-0.08390.32840.0811-0.00540.2911-0.06530.1142-4.987-29.84494.3936
233.7264-3.3002-0.04984.0199-1.47074.0584-0.5689-0.68060.29821.13970.5432-0.4385-0.8448-0.2689-0.08580.46740.1278-0.12590.4017-0.12520.2923-5.5329-30.435611.39
242.2419-0.9889-0.58843.39960.20232.1360.0139-0.39920.0230.39510.1680.02030.0931-0.3865-0.11940.28140.038-0.01290.3096-0.02160.1448-5.192-41.88488.3841
256.42342.3503-1.8283.5627-0.74225.2162-0.1327-0.19130.05350.40740.1035-0.4662-0.22410.17310.05280.1260.0258-0.08490.1664-0.01840.21838.3469-44.4334-0.7019
264.9877-0.6343-2.50224.7711-1.68682.1369-0.0474-0.2467-0.05850.18850.1047-0.8411-0.150.3572-0.05250.12250.0156-0.06650.2678-0.0430.272215.152-44.6451-5.8078
274.15450.47741.0451.4691.05272.2045-0.1018-0.7912-0.22940.42790.01530.17630.4941-0.07910.08670.3459-0.02830.00160.27460.10030.1572-8.5733-63.7692-5.2818
280.76261.08220.10261.8636-0.09362.80080.0067-0.10390.06820.0066-0.0008-0.0482-0.16690.1103-0.01610.16350.031-0.00690.13580.00770.17530.4834-59.0491-25.9416
291.4113-0.4008-0.35732.00780.27293.04240.006-0.0761-0.08770.1264-0.0176-0.06620.2740.12890.01610.1920.0561-0.00260.09460.01150.14990.4788-71.259-29.7883
305.0895-0.533-0.52192.6660.28052.9090.2113-0.4606-0.50710.336-0.17080.36780.8261-0.2620.02640.2934-0.0694-0.00930.17480.0810.1742-13.356-70.059-11.8446
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resseq 4:37)
2X-RAY DIFFRACTION2chain A and (resseq 38:86)
3X-RAY DIFFRACTION3chain A and (resseq 87:127)
4X-RAY DIFFRACTION4chain A and (resseq 128:179)
5X-RAY DIFFRACTION5chain A and (resseq 180:217)
6X-RAY DIFFRACTION6chain B and (resseq 4:17)
7X-RAY DIFFRACTION7chain B and (resseq 18:37)
8X-RAY DIFFRACTION8chain B and (resseq 38:56)
9X-RAY DIFFRACTION9chain B and (resseq 57:70)
10X-RAY DIFFRACTION10chain B and (resseq 71:86)
11X-RAY DIFFRACTION11chain B and (resseq 87:139)
12X-RAY DIFFRACTION12chain B and (resseq 140:152)
13X-RAY DIFFRACTION13chain B and (resseq 153:165)
14X-RAY DIFFRACTION14chain B and (resseq 166:179)
15X-RAY DIFFRACTION15chain B and (resseq 180:197)
16X-RAY DIFFRACTION16chain B and (resseq 198:217)
17X-RAY DIFFRACTION17chain C and (resseq 5:17)
18X-RAY DIFFRACTION18chain C and (resseq 18:37)
19X-RAY DIFFRACTION19chain C and (resseq 38:70)
20X-RAY DIFFRACTION20chain C and (resseq 71:85)
21X-RAY DIFFRACTION21chain C and (resseq 86:102)
22X-RAY DIFFRACTION22chain C and (resseq 103:139)
23X-RAY DIFFRACTION23chain C and (resseq 140:152)
24X-RAY DIFFRACTION24chain C and (resseq 153:179)
25X-RAY DIFFRACTION25chain C and (resseq 180:197)
26X-RAY DIFFRACTION26chain C and (resseq 198:217)
27X-RAY DIFFRACTION27chain D and (resseq 4:37)
28X-RAY DIFFRACTION28chain D and (resseq 38:86)
29X-RAY DIFFRACTION29chain D and (resseq 87:179)
30X-RAY DIFFRACTION30chain D and (resseq 180:217)

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