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- PDB-6bnj: Human hypoxanthine guanine phosphoribosyltransferase in complex w... -

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Basic information

Entry
Database: PDB / ID: 6bnj
TitleHuman hypoxanthine guanine phosphoribosyltransferase in complex with [3R,4R]-4-guanin-9-yl-3-((R)-2-hydroxy-2-phosphonoethyl)oxy-1-N-(phosphonopropionyl)pyrrolidine
ComponentsHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE/INHIBITOR / enzyme / inhibitor / nucleoside phosphonate / purine salvage / malaria / phosphoribosyltransferase / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


adenine metabolic process / Defective HPRT1 disrupts guanine and hypoxanthine salvage / GMP catabolic process / guanine salvage / hypoxanthine metabolic process / hypoxanthine salvage / cerebral cortex neuron differentiation / positive regulation of dopamine metabolic process / lymphocyte proliferation / hypoxanthine phosphoribosyltransferase ...adenine metabolic process / Defective HPRT1 disrupts guanine and hypoxanthine salvage / GMP catabolic process / guanine salvage / hypoxanthine metabolic process / hypoxanthine salvage / cerebral cortex neuron differentiation / positive regulation of dopamine metabolic process / lymphocyte proliferation / hypoxanthine phosphoribosyltransferase / IMP metabolic process / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / grooming behavior / IMP salvage / Purine salvage / striatum development / AMP salvage / dopaminergic neuron differentiation / purine nucleotide biosynthetic process / Azathioprine ADME / purine ribonucleoside salvage / dendrite morphogenesis / dopamine metabolic process / central nervous system neuron development / 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-WPG / Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.909 Å
AuthorsKeough, D.T. / Rejman, D. / Guddat, L.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
nhmrc1030353 Australia
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Design of Plasmodium vivax Hypoxanthine-Guanine Phosphoribosyltransferase Inhibitors as Potential Antimalarial Therapeutics.
Authors: Keough, D.T. / Rejman, D. / Pohl, R. / Zbornikova, E. / Hockova, D. / Croll, T. / Edstein, M.D. / Birrell, G.W. / Chavchich, M. / Naesens, L.M.J. / Pierens, G.K. / Brereton, I.M. / Guddat, L.W.
History
DepositionNov 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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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)100,37316
Polymers98,1934
Non-polymers2,18012
Water9,656536
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, All crystal forms of this enzyme are a tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11760 Å2
ΔGint-96 kcal/mol
Surface area29720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.620, 93.942, 130.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Hypoxanthine-guanine phosphoribosyltransferase / / HGPRTase


Mass: 24548.281 Da / Num. of mol.: 4
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-WPG / (3-{(3R,4R)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-4-[(2R)-2-hydroxy-2-phosphonoethoxy]pyrrolidin-1-yl}-3-oxopropy l)phosphonic acid / [3R,4R]-4-guanin-9-yl-3-((R)-2-hydroxy-2-phosphonoethyl)oxy-1-N-(phosphonopropionyl)pyrrolidine


Mass: 496.306 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H22N6O10P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 536 / 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: 2.31 Å3/Da / Density % sol: 46.71 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 0.3 M sodium acetate, 17.5% PEG 3350 and, for 5, 0.2 M sodium acetate, 20% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.909→42.4 Å / Num. obs: 69600 / % possible obs: 99.7 % / Redundancy: 7.12 % / Net I/σ(I): 15.7
Reflection shellResolution: 1.909→1.95 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.182 / Num. unique obs: 4279 / Rpim(I) all: 0.08 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.909→42.4 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.43 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2083 2000 3 %
Rwork0.1759 --
obs0.1769 66772 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.909→42.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6477 0 136 536 7149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0157077
X-RAY DIFFRACTIONf_angle_d1.5339673
X-RAY DIFFRACTIONf_dihedral_angle_d16.6412846
X-RAY DIFFRACTIONf_chiral_restr0.0721084
X-RAY DIFFRACTIONf_plane_restr0.0071229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9094-1.95710.2921380.264478X-RAY DIFFRACTION98
1.9571-2.010.25231420.20654579X-RAY DIFFRACTION100
2.01-2.06920.24681390.20084545X-RAY DIFFRACTION100
2.0692-2.13590.23561430.18974603X-RAY DIFFRACTION100
2.1359-2.21230.20491420.18154596X-RAY DIFFRACTION100
2.2123-2.30090.24991410.19374577X-RAY DIFFRACTION100
2.3009-2.40560.2141420.18244599X-RAY DIFFRACTION100
2.4056-2.53240.22991420.18024596X-RAY DIFFRACTION100
2.5324-2.6910.21691440.18184649X-RAY DIFFRACTION100
2.691-2.89870.19571420.1844613X-RAY DIFFRACTION100
2.8987-3.19040.1941440.17484640X-RAY DIFFRACTION100
3.1904-3.65180.18721440.16224691X-RAY DIFFRACTION100
3.6518-4.60.17251460.14434701X-RAY DIFFRACTION100
4.6-42.41060.19621510.15974905X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.03420.3495-1.01650.8813-1.05221.38180.0059-0.42540.07310.0896-0.09630.3763-0.1075-0.40240.04710.13540.03880.03220.32-0.01620.1647-39.4718-15.764240.8873
20.8869-0.17420.27381.7518-0.82052.767-0.0496-0.05810.09770.18550.00510.2196-0.32260.0380.0330.15720.05080.0060.1699-0.03740.1209-29.4841-1.790936.6925
30.8966-0.3236-0.02051.18620.01161.8109-0.063-0.0321-0.1218-0.02760.00260.03180.1338-0.2210.04780.0889-0.03920.01750.1097-0.02660.1429-29.6081-27.041426.8268
43.1408-2.4261.37172.7269-1.5922.13280.08850.1547-0.0393-0.1356-0.1805-0.0797-0.04380.13480.06210.1078-0.01750.01990.1297-0.02830.136-23.6416-24.09425.7969
53.4697-0.07151.42310.24810.66372.55110.0699-0.5151-0.2618-0.03050.058-0.00320.3921-0.5311-0.1530.1959-0.08650.02070.2071-0.01650.2129-25.1148-30.195519.9462
62.1804-0.5455-0.12742.69410.4431.63890.11170.60790.2771-0.5211-0.0528-0.1876-0.0769-0.25050.00370.1535-0.04230.01690.3112-0.03690.1581-36.5716-24.231516.7505
70.84080.5209-0.74316.44041.33933.87790.00860.14320.12390.36590.02030.37940.0942-0.45390.16720.1425-0.1-0.03280.4102-0.05570.1397-43.61-25.404214.0169
81.3454-0.3590.27293.88512.16684.0015-0.14810.1469-0.211-0.04690.07250.30970.3399-0.10150.11390.1582-0.05040.00490.2134-0.06190.169-38.2979-27.199622.4118
91.89120.01870.24150.21350.53761.4563-0.06330.1949-0.118-0.0466-0.00290.3214-0.1314-0.41780.05660.13350.00040.01070.3253-0.05630.2756-45.8026-21.722128.5534
101.29110.26450.10742.6821-1.79762.1884-0.08210.13570.10760.02490.11940.1603-0.1718-0.5329-0.06070.13560.0559-0.0110.1752-0.02670.14-37.3369-8.736328.6737
110.78620.3778-0.56563.21950.06222.5458-0.00940.10580.01760.0551-0.04170.2418-0.3302-0.18140.03630.12140.0477-0.0080.1253-0.01080.1292-33.8408-1.116529.2083
121.8747-1.10820.33432.02790.62981.69240.0089-0.2777-0.24550.2891-0.11230.33250.1407-0.34660.11870.1484-0.02070.05450.28180.01310.1777-30.2838-22.898348.6414
132.45530.2055-0.02460.7688-0.11931.9919-0.0099-0.09980.05140.02940.031-0.0746-0.09630.0826-0.00860.12290.00570.00080.1037-0.03030.1093-11.8936-9.297745.7637
142.8021-0.01130.71492.16021.55473.0391-0.0728-0.49040.04620.38140.1333-0.180.0109-0.0135-0.04770.16770.0089-0.02110.2424-0.07980.247-2.2792-9.970453.0367
151.34350.15120.76021.53120.90241.1971-0.1095-0.2676-0.08060.1920.1180.00880.062-0.1571-0.00030.16270.02850.01870.2157-0.00110.1089-17.5332-15.747758.293
163.27190.5776-1.08051.15850.93472.6265-0.1009-0.0863-0.2748-0.3932-0.1321-0.25360.06790.58680.2620.15010.04910.04110.33250.02710.17411.7266-21.758615.1725
171.3969-0.69380.39342.3377-1.00471.56790.05860.1037-0.1467-0.2083-0.0121-0.12670.15430.095-0.0490.09920.00370.00960.141-0.03070.1213-9.175-21.25921.1648
182.0219-0.18580.5781.14670.14092.770.0342-0.0054-0.0605-0.0445-0.0568-0.0569-0.0123-0.10740.03340.09350.00430.0240.0975-0.00570.1018-19.9063-8.906919.8784
191.9891-0.6145-0.06172.4228-1.97231.7784-0.00340.2532-0.0287-0.2628-0.02430.05720.0968-0.22780.01390.14440.02050.04050.15970.00730.1512-24.8738-4.133814.8938
201.5913-0.87820.4981.3481-0.26641.0870.03350.15250.017-0.05110.0093-0.12640.01640.0815-0.05810.11910.00550.03310.11480.0150.0806-13.4087-7.23786.5541
212.92221.17780.30862.57780.37032.04460.0260.471-0.3222-0.1370.0049-0.07870.21790.0961-0.03420.15240.0262-0.00140.1521-0.04880.1381-11.5293-24.306210.4888
221.6787-0.3460.08612.18540.24040.03450.32850.629-0.6696-0.26660.0139-0.03120.44210.1047-0.21230.31730.0468-0.06360.2524-0.10620.3022-13.5187-32.194612.1203
233.0774-0.8742-0.01481.38350.30282.73320.0763-0.0361-0.36030.0491-0.17450.00720.19450.10790.09510.0818-0.00960.02670.2075-0.02990.18093.9348-24.380326.2521
241.3783-0.25850.08082.194-0.03922.1502-0.01370.0147-0.009-0.13770.0551-0.1081-0.03460.1532-0.03630.05010.0105-0.00360.1276-0.03020.1088-2.0383-20.754232.7412
252.4549-0.32930.46341.31380.50042.5283-0.0471-0.1506-0.16150.2220.0417-0.0240.0649-0.0660.02860.130.01060.00080.1320.01630.1333-8.2372-28.774644.4028
261.9143-1.3073-0.0022.1805-1.08562.38110.175-0.1024-0.6361-0.01420.08810.04650.5454-0.1411-0.24050.23630.01010.00970.21540.02440.2702-13.6011-33.426945.9165
273.51931.00140.01442.42110.3911.5380.2651-1.32920.09980.8621-0.2352-0.0494-0.06140.4530.00280.36650.0423-0.01810.49550.03710.27161.5656-31.415152.1534
282.20770.37160.11372.48-0.40732.04820.0972-0.5711-0.41090.4729-0.1919-0.32720.32020.42980.09540.29550.0524-0.02080.34040.09370.2755.9728-35.632244.8112
291.5607-0.3087-0.09051.4246-0.42031.401-0.0097-0.18110.13380.10350.095-0.2397-0.15090.5522-0.04570.0988-0.0427-0.0150.2485-0.04710.19247.896-14.025437.9244
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 37 )
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 70 )
4X-RAY DIFFRACTION4chain 'A' and (resid 71 through 86 )
5X-RAY DIFFRACTION5chain 'A' and (resid 87 through 100 )
6X-RAY DIFFRACTION6chain 'A' and (resid 101 through 139 )
7X-RAY DIFFRACTION7chain 'A' and (resid 140 through 152 )
8X-RAY DIFFRACTION8chain 'A' and (resid 153 through 165 )
9X-RAY DIFFRACTION9chain 'A' and (resid 166 through 179 )
10X-RAY DIFFRACTION10chain 'A' and (resid 180 through 197 )
11X-RAY DIFFRACTION11chain 'A' and (resid 198 through 217 )
12X-RAY DIFFRACTION12chain 'B' and (resid 3 through 37 )
13X-RAY DIFFRACTION13chain 'B' and (resid 38 through 85 )
14X-RAY DIFFRACTION14chain 'B' and (resid 86 through 127 )
15X-RAY DIFFRACTION15chain 'B' and (resid 128 through 217 )
16X-RAY DIFFRACTION16chain 'C' and (resid 4 through 17 )
17X-RAY DIFFRACTION17chain 'C' and (resid 18 through 56 )
18X-RAY DIFFRACTION18chain 'C' and (resid 57 through 85 )
19X-RAY DIFFRACTION19chain 'C' and (resid 86 through 127 )
20X-RAY DIFFRACTION20chain 'C' and (resid 128 through 179 )
21X-RAY DIFFRACTION21chain 'C' and (resid 180 through 197 )
22X-RAY DIFFRACTION22chain 'C' and (resid 198 through 217 )
23X-RAY DIFFRACTION23chain 'D' and (resid 0 through 20 )
24X-RAY DIFFRACTION24chain 'D' and (resid 21 through 56 )
25X-RAY DIFFRACTION25chain 'D' and (resid 57 through 85 )
26X-RAY DIFFRACTION26chain 'D' and (resid 86 through 100 )
27X-RAY DIFFRACTION27chain 'D' and (resid 101 through 139 )
28X-RAY DIFFRACTION28chain 'D' and (resid 140 through 179 )
29X-RAY DIFFRACTION29chain 'D' and (resid 180 through 217 )

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