[English] 日本語
Yorodumi
- PDB-3gep: Human hypoxanthine guanine phosphoribosyltranserfase in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gep
TitleHuman hypoxanthine guanine phosphoribosyltranserfase in complex with (S)-9-(3-hydroxy-2-phosphonylmethoxypropyl)guanine
ComponentsHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE / phosphoribosyltransferase / acyclic nucleoside phosphonate / purine salvage pathway / malarial chemotherapeutic / Acetylation / Cytoplasm / Disease mutation / Glycosyltransferase / Gout / Magnesium / Metal-binding / Purine salvage
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-24H / Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 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 25, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,6014
Polymers48,9622
Non-polymers6382
Water3,027168
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)99,2028
Polymers97,9254
Non-polymers1,2774
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area9300 Å2
ΔGint-29 kcal/mol
Surface area35120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.122, 72.590, 51.282
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
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-24H / {[(1S)-2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-1-(hydroxymethyl)ethoxy]methyl}phosphonic acid


Mass: 319.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N5O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M citrate, 10% isopropanol, 29% PEG 4000, 3.9mM (RS)- HPMPG, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
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 5, 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→29.63 Å / Num. all: 13343 / Num. obs: 13343 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 9.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 4.5 / Num. unique all: 1334 / Rsym value: 0.179 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
REFMAC5.2.0019refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z7G

1z7g


Resolution: 2.6→29.63 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.881 / Cross valid method: THROUGHOUT / ESU R Free: 0.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2983 666 5.1 %RANDOM
Rwork0.24725 ---
obs0.24984 12298 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2--0.15 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3283 0 42 168 3493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223394
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.9934601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2875422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40223.732142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.2815583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5931521
X-RAY DIFFRACTIONr_chiral_restr0.2340.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022521
X-RAY DIFFRACTIONr_nbd_refined0.2070.21521
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22247
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2185
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.221
X-RAY DIFFRACTIONr_mcbond_it3.7711.52102
X-RAY DIFFRACTIONr_mcangle_it5.52123389
X-RAY DIFFRACTIONr_scbond_it1.74931292
X-RAY DIFFRACTIONr_scangle_it2.8894.51210
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.5 48 -
Rwork0.333 871 -
obs--99.14 %

+
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