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- PDB-1d6n: TERNARY COMPLEX STRUCTURE OF HUMAN HGPRTASE, PRPP, MG2+, AND THE ... -

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Basic information

Entry
Database: PDB / ID: 1d6n
TitleTERNARY COMPLEX STRUCTURE OF HUMAN HGPRTASE, PRPP, MG2+, AND THE INHIBITOR HPP REVEALS THE INVOLVEMENT OF THE FLEXIBLE LOOP IN SUBSTRATE BINDING
ComponentsPROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)
KeywordsTRANSFERASE / HGPRTASE
Function / homology
Function and homology information


adenine metabolic process / Defective HPRT1 disrupts guanine and hypoxanthine salvage / GMP catabolic process / cerebral cortex neuron differentiation / hypoxanthine salvage / positive regulation of dopamine metabolic process / lymphocyte proliferation / hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process ...adenine metabolic process / Defective HPRT1 disrupts guanine and hypoxanthine salvage / GMP catabolic process / cerebral cortex neuron differentiation / hypoxanthine salvage / positive regulation of dopamine metabolic process / lymphocyte proliferation / hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process / IMP metabolic process / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / grooming behavior / Purine salvage / 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 / 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
3H-PYRAZOLO[4,3-D]PYRIMIDIN-7-OL / Chem-PRP / Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsBalendiran, G.K.
CitationJournal: Protein Sci. / Year: 1999
Title: Ternary complex structure of human HGPRTase, PRPP, Mg2+, and the inhibitor HPP reveals the involvement of the flexible loop in substrate binding.
Authors: Balendiran, G.K. / Molina, J.A. / Xu, Y. / Torres-Martinez, J. / Stevens, R. / Focia, P.J. / Eakin, A.E. / Sacchettini, J.C. / Craig III, S.P.
History
DepositionOct 14, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.6Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.7Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.8Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)
B: PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1448
Polymers48,0432
Non-polymers1,1016
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-48 kcal/mol
Surface area19530 Å2
MethodPISA
2
A: PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)
B: PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)
hetero molecules

A: PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)
B: PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,28816
Polymers96,0864
Non-polymers2,20212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area12800 Å2
ΔGint-111 kcal/mol
Surface area35470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.560, 65.850, 51.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE) / HGPRT


Mass: 24021.609 Da / Num. of mol.: 2 / Mutation: K68A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Plasmid: PBACPRT-68A / Production host: Escherichia coli (E. coli)
References: UniProt: P00492, hypoxanthine phosphoribosyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PPO / 3H-PYRAZOLO[4,3-D]PYRIMIDIN-7-OL


Mass: 136.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N4O
#4: Sugar ChemComp-PRP / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose / ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribose / 1-O-pyrophosphono-5-O-phosphono-D-ribose / 1-O-pyrophosphono-5-O-phosphono-ribose


Type: D-saccharide / Mass: 390.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H13O14P3
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14.3 mg/mlprotein1drop
21.4 mMHPP1drop
31.4 mMPRPP1drop
41.4 mM1dropMgCl2
543 mMHEPES1drop
613 %PEG40001drop
7100 mMHEPES1reservoir
830 %PEG40001reservoir

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 9320 / % possible obs: 76.2 %
Reflection
*PLUS
Rmerge(I) obs: 0.112

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-GENdata reduction
X-GENdata scaling
X-PLORphasing
RefinementResolution: 2.7→20 Å / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.174 / Rfactor obs: 0.174
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 69 49 3490
Software
*PLUS
Name: TNT / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.02
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg2.5

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