[English] 日本語
Yorodumi
- PDB-4ijq: Human hypoxanthine-guanine phosphoribosyltransferase in complex w... -

+
Open data


ID or keywords:

Loading...

-
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 / GMP catabolic process / adenine metabolic process / cerebral cortex neuron differentiation / positive regulation of dopamine metabolic process / hypoxanthine salvage / hypoxanthine phosphoribosyltransferase / lymphocyte proliferation / IMP metabolic process / guanine phosphoribosyltransferase activity ...Defective HPRT1 disrupts guanine and hypoxanthine salvage / GMP catabolic process / adenine metabolic process / cerebral cortex neuron differentiation / positive regulation of dopamine metabolic process / hypoxanthine salvage / hypoxanthine phosphoribosyltransferase / lymphocyte proliferation / IMP metabolic process / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / Purine salvage / grooming behavior / GMP salvage / IMP salvage / striatum development / AMP salvage / dopaminergic neuron differentiation / purine nucleotide biosynthetic process / purine ribonucleoside salvage / Azathioprine ADME / 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-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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more