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1d6n

TERNARY COMPLEX STRUCTURE OF HUMAN HGPRTASE, PRPP, MG2+, AND THE INHIBITOR HPP REVEALS THE INVOLVEMENT OF THE FLEXIBLE LOOP IN SUBSTRATE BINDING

Method: X-RAY DIFFRACTION Dmax: 70.3 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)

Homo sapiens

UniProt P00492

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 4–217 Chain B； UniProt 4–217 Mutation：K68A MG MAGNESIUM ION × 2 PPO 3H-PYRAZOLO[4,3-D]PYRIMIDIN-7-OL × 2 PRP 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose × 2 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.50 Resolution 2.70 Å R-free 0.278
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 4–217 Chain B； UniProt 4–217 Mutation：K68A MG MAGNESIUM ION × 4 PPO 3H-PYRAZOLO[4,3-D]PYRIMIDIN-7-OL × 4 PRP 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose × 4 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.50 Resolution 2.70 Å R-free 0.278

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1D6N Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BZY HUMAN HGPRTASE WITH TRANSITION STATE INHIBITOR Deposited 1998-11-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–217（217 aa）
Chain B 1–217（217 aa）
Chain C 1–217（217 aa）
Chain D 1–217（217 aa）
Not recorded MG MAGNESIUM ION × 8 IMU PHOSPHORIC ACID MONO-[5-(2-AMINO-4-OXO-4,5-DIHYDRO-3H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)-3,4-DIHYDROXY-PYRROLIDIN-2-YLMETHYL] ESTER × 4 POP PYROPHOSPHATE 2- × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；pH 4.6
Resolution 2.00 Å R-free 0.249
1HMP THE CRYSTAL STRUCTURE OF HUMAN HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE WITH BOUND GMP Deposited 1994-06-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–217（217 aa）
Chain B 1–217（217 aa）
Not recorded 5GP GUANOSINE-5'-MONOPHOSPHATE × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
1Z7G Free human HGPRT Deposited 2005-03-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–217（217 aa）
Chain B 1–217（217 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；0.2 M ammonium acetate, 0.1 M sodium acetate, 30% PEG4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.90 Å R-free 0.254
1Z7G Free human HGPRT Deposited 2005-03-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain C 1–217（217 aa）
Chain D 1–217（217 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；0.2 M ammonium acetate, 0.1 M sodium acetate, 30% PEG4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.90 Å R-free 0.254
2VFA Crystal structure of a chimera of Plasmodium falciparum and human hypoxanthine-guanine phosphoribosyl transferases Deposited 2007-11-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 49–160（112 aa） Fragment：RESIDUES 1-56,49-160,171-231
Chain B 49–160（112 aa） Fragment：RESIDUES 1-56,49-160,171-231
Not recorded 5GP GUANOSINE-5'-MONOPHOSPHATE × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；0.1M TRIS PH 8.0, 2.0M AMMONIUM SULPHATE
Resolution 2.80 Å R-free 0.278
3GEP Human hypoxanthine guanine phosphoribosyltranserfase in complex with (S)-9-(3-hydroxy-2-phosphonylmethoxypropyl)guanine Deposited 2009-02-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–218（217 aa）
Chain B 2–218（217 aa）
Not recorded 24H {[(1S)-2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-1-(hydroxymethyl)ethoxy]methyl}phosphonic acid × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M citrate, 10% isopropanol, 29% PEG 4000, 3.9mM (RS)- HPMPG, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.298
3GGC Human hypoxanthine-guanine phosphoribosyltransferase in complex with 9-(2-phosphonoethoxyethyl)hypoxanthine Deposited 2009-02-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–218（217 aa）
Chain B 2–218（217 aa）
Not recorded H26 {2-[2-(6-oxo-1,6-dihydro-9H-purin-9-yl)ethoxy]ethyl}phosphonic acid × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.1M citrate, 10% iso-propanol, 29% PEG 4000, pH 6.5
Resolution 2.78 Å R-free 0.285
3GGJ Human hypoxanthine-guanine phosphoribosyltransferase in complex with 9-(2-phosphonoethoxyethyl)guanine Deposited 2009-02-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–218（217 aa）
Chain B 2–218（217 aa）
Not recorded 25H {2-[2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)ethoxy]ethyl}phosphonic acid × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M citrate, 10% iso-propanol, 29% PEG 4000, 3.3mM inhibitor , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.295
4IJQ Human hypoxanthine-guanine phosphoribosyltransferase in complex with [(2-((Guanine-9H-yl)methyl)propane-1,3-diyl)bis(oxy)]bis(methylene))diphosphonic acid Deposited 2012-12-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–218（217 aa） Fragment：human HGPRT, UNP residues 4-217
Chain B 2–218（217 aa） Fragment：human HGPRT, UNP residues 4-217
Chain C 2–218（217 aa） Fragment：human HGPRT, UNP residues 4-217
Chain D 2–218（217 aa） Fragment：human HGPRT, UNP residues 4-217
Not recorded SV2 [{2-[(guanine-9-yl)methyl]propane-1,3-diyl}bis(oxymethylene)]bis(phosphonic acid) × 4 SO4 SULFATE ION × 4 MG MAGNESIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.2M LiSO4, 30% PEG5000MME, 0.1M Tris-HCl, 0.88mM ligand, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.00 Å R-free 0.223
4KN6 Crystal structure of human hypoxanthine-guanine phosphoribosyltransferase in complex with 6-fluoro-3-hydroxy-2-pyrazinecarboxamide (T-705) ribose-5'-monophosphate Deposited 2013-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–218（216 aa）
Not recorded 1RP 6-fluoro-3-oxo-4-(5-O-phosphono-beta-D-ribofuranosyl)-3,4-dihydropyrazine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；0.2 M sodium chloride, 1 M sodium/potassium tartrate, 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP
Resolution 2.73 Å R-free 0.278
4KN6 Crystal structure of human hypoxanthine-guanine phosphoribosyltransferase in complex with 6-fluoro-3-hydroxy-2-pyrazinecarboxamide (T-705) ribose-5'-monophosphate Deposited 2013-05-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3–218（216 aa）
Not recorded 1RP 6-fluoro-3-oxo-4-(5-O-phosphono-beta-D-ribofuranosyl)-3,4-dihydropyrazine-2-carboxamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；0.2 M sodium chloride, 1 M sodium/potassium tartrate, 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP
Resolution 2.73 Å R-free 0.278
4RAB Aza-acyclic nucleoside phosphonates containing a second phosphonate group as inhibitors of the human, Plasmodium falciparum and vivax 6-oxopurine phosphoribosyltransferases and their pro-drugs as antimalarial agents Deposited 2014-09-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–218（217 aa）
Chain B 2–218（217 aa）
Chain C 2–218（217 aa）
Chain D 2–218（217 aa）
Not recorded 3L3 [(E)-2-(2-{[2-(2-amino-8-bromo-6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl][(E)-2-phosphonoethenyl]amino}ethoxy)ethenyl]phosphonic acid × 4 MG MAGNESIUM ION × 6 PO4 PHOSPHATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；20% PEG 3350, 0.2 M sodium acetate, VAPOR DIFFUSION, HANGING DROP
Resolution 2.26 Å R-free 0.231
4RAC Aza-acyclic nucleoside phosphonates containing a second phosphonate group as inhibitors of the human, Plasmodium falciparum and vivax 6-oxopurine phosphoribosyltransferases and their pro-drugs as antimalarial agents Deposited 2014-09-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–218（217 aa）
Chain B 2–218（217 aa）
Chain C 2–218（217 aa）
Chain D 2–218（217 aa）
Not recorded 3L4 [(2-{[2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl][(E)-2-phosphonoethenyl]amino}ethoxy)methyl]phosphonic acid × 4 MG MAGNESIUM ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；1 M sodium/potassium tartrate, 0.2 M NaCl, 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP
Resolution 2.05 Å R-free 0.244
4RAD Aza-acyclic nucleoside phosphonates containing a second phosphonate group as inhibitors of the human, Plasmodium falciparum and vivax 6-oxopurine phosphoribosyltransferases and their pro-drugs as antimalarial agents Deposited 2014-09-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–218（217 aa）
Chain B 2–218（217 aa）
Chain C 2–218（217 aa）
Chain D 2–218（217 aa）
Not recorded 3L5 (2-{[2-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)ethyl][2-(2-phosphonoethoxy)ethyl]amino}ethyl)phosphonic acid × 4 MG MAGNESIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；1 M sodium/potassium tartrate, 0.2 M NaCl, 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP
Resolution 2.00 Å R-free 0.259
4RAD Aza-acyclic nucleoside phosphonates containing a second phosphonate group as inhibitors of the human, Plasmodium falciparum and vivax 6-oxopurine phosphoribosyltransferases and their pro-drugs as antimalarial agents Deposited 2014-09-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain E 2–218（217 aa）
Chain F 2–218（217 aa）
Chain G 2–218（217 aa）
Chain H 2–218（217 aa）
Not recorded 3L5 (2-{[2-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)ethyl][2-(2-phosphonoethoxy)ethyl]amino}ethyl)phosphonic acid × 4 MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；1 M sodium/potassium tartrate, 0.2 M NaCl, 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP
Resolution 2.00 Å R-free 0.259
4RAN Aza-acyclic nucleoside phosphonates containing a second phosphonate group as inhibitors of the human, Plasmodium falciparum and vivax 6-oxopurine phosphoribosyltransferases and their pro-drugs as antimalarial agents Deposited 2014-09-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–218（217 aa）
Chain B 2–218（217 aa）
Chain C 2–218（217 aa）
Chain D 2–218（217 aa）
Not recorded 3L6 (2-{[2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl](3-aminopropyl)amino}ethyl)phosphonic acid × 4 MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；20% PEG 3000, 0.2 M calcium acetate, VAPOR DIFFUSION, HANGING DROP
Resolution 2.55 Å R-free 0.246
4RAO Aza-acyclic nucleoside phosphonates containing a second phosphonate group as inhibitors of the human, Plasmodium falciparum and vivax 6-oxopurine phosphoribosyltransferases and their pro-drugs as antimalarial agents Deposited 2014-09-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–218（217 aa）
Chain B 2–218（217 aa）
Chain C 2–218（217 aa）
Chain D 2–218（217 aa）
Not recorded 3L7 (2-{[2-(6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl](2-{[(E)-2-phosphonoethenyl]oxy}ethyl)amino}ethyl)phosphonic acid × 4 MG MAGNESIUM ION × 8 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.87 Å R-free 0.230
4RAQ Aza-acyclic nucleoside phosphonates containing a second phosphonate group as inhibitors of the human, Plasmodium falciparum and vivax 6-oxopurine phosphoribosyltransferases and their pro-drugs as antimalarial agents Deposited 2014-09-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–218（217 aa）
Chain B 2–218（217 aa）
Chain C 2–218（217 aa）
Chain D 2–218（217 aa）
Not recorded 3L8 [(2-{[2-(6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl](2-phosphonoethyl)amino}ethoxy)methyl]phosphonic acid × 4 MG MAGNESIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；0.2 M calcium acetate, 0.1 M Tris-HCl, pH 7.5, 20% PEG3000, VAPOR DIFFUSION, HANGING DROP
Resolution 2.53 Å R-free 0.269
5BRN Human HGPRT in complex with (S)-HPEPHx, an acyclic nucleoside phosphonate Deposited 2015-05-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–218（218 aa）
Chain B 1–218（218 aa）
Chain C 1–218（218 aa）
Chain D 1–218（218 aa）
Mutation：C22A, C105A, C205A Mutation：C22A, C105A, C205A Mutation：C22A, C105A, C205A Mutation：C22A, C105A, C205A MG MAGNESIUM ION × 4 4X2 (2-{[(2S)-1-hydroxy-3-(6-oxo-1,6-dihydro-9H-purin-9-yl)propan-2-yl]oxy}ethyl)phosphonic acid × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；20% PEG3000, 0.2 M calcium acetate, 0.1 M Tris-HCl pH 7.4
Resolution 2.30 Å R-free 0.292
5BSK Human HGPRT in complex with (S)-HPEPG, an acyclic nucleoside phosphonate Deposited 2015-06-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–218（218 aa）
Chain B 1–218（218 aa）
Chain C 1–218（218 aa）
Chain D 1–218（218 aa）
Mutation：C22A, C105A, C205A Mutation：C22A, C105A, C205A Mutation：C22A, C105A, C205A Mutation：C22A, C105A, C205A 4X7 (2-{[(2S)-1-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3-hydroxypropan-2-yl]oxy}ethyl)phosphonic acid × 4 MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；15% PEG 3000, 0.2 M calcium acetate, 0.1 M Tris-HCl pH 7.4
Resolution 2.61 Å R-free 0.268
5HIA Human hypoxanthine-guanine phosphoribosyltransferase in complex with [3R,4R]-4-guanin-9-yl-3-((S)-2-hydroxy-2-phosphonoethyl)oxy-1-N-(phosphonopropionyl)pyrrolidine Deposited 2016-01-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–218（218 aa）
Chain B 1–218（218 aa）
Chain C 1–218（218 aa）
Chain D 1–218（218 aa）
Mutation：C23A,C206A Mutation：C23A,C206A Mutation：C23A,C206A Mutation：C23A,C206A YPG [3-[(3~{R},4~{R})-3-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[(2~{S})-2-oxidanyl-2-phosphono-ethoxy]pyrrolidin-1-y l]-3-oxidanylidene-propyl]phosphonic acid × 4 MG MAGNESIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.3 M sodium acetate, 17.5% PEG 3350
Resolution 1.77 Å R-free 0.232
5W8V HUMAN HGPRT in complex with [(2-[(guanin-9-yl)methyl]propane-1,3-diyl)bis(oxy)]bis(methylene)diphosphonic acid Deposited 2017-06-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 5–218（214 aa）
Chain B 5–218（214 aa）
Chain C 5–218（214 aa）
Chain D 5–218（214 aa）
Not recorded 9YP {[(2R)-2-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)methyl]-3-(2-phosphonoethoxy)propoxy]methyl}phosphonic acid × 4 MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；20% PEG 3350, 0.2 M sodium bromide, 0.1 M Bis-tris propane, pH 7.5.
Resolution 2.35 Å R-free 0.249
6BNJ Human hypoxanthine guanine phosphoribosyltransferase in complex with [3R,4R]-4-guanin-9-yl-3-((R)-2-hydroxy-2-phosphonoethyl)oxy-1-N-(phosphonopropionyl)pyrrolidine Deposited 2017-11-16 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–218（218 aa）
Chain B 1–218（218 aa）
Chain C 1–218（218 aa）
Chain D 1–218（218 aa）
Not recorded 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 × 4 MG MAGNESIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；0.3 M sodium acetate, 17.5% PEG 3350 and, for 5, 0.2 M sodium acetate, 20% PEG 3350.
Resolution 1.91 Å R-free 0.208
7SAN Crystal structure of human hypoxanthine guanine phosphoribzosyltransferase in complex with (4S,7S)-7-hydroxy-4-((guanin-9-yl)methyl)-2,5-dioxaheptan-1,7-diphosphonate Deposited 2021-09-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–218（217 aa）
Chain B 2–218（217 aa）
Chain C 2–218（217 aa）
Chain D 2–218（217 aa）
Mutation：C22A, C105A, C205A Mutation：C22A, C105A, C205A Mutation：C22A, C105A, C205A Mutation：C22A, C105A, C205A 8QI ({(2S)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2-[(2S)-2-hydroxy-2-phosphonoethoxy]propoxy}methyl)phosphonic acid × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.1 M Bis-tris propane, pH 7.4, 0.1 M sodium citrate, 17.5% PEG 3350
Resolution 2.58 Å R-free 0.257
8TPV Structure of human hypoxanthine guanine phosphoribzosyltransferase in complex with [2S,4R]-4-Guanin-9-yl-2-(2-phosphonoethoxymethyl)-1-N-(3-phosphonopropionyl)pyrrolidine Deposited 2023-08-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 4–218（215 aa）
Chain B 4–218（215 aa）
Chain C 4–218（215 aa）
Chain D 4–218（215 aa）
Mutation：C22A C105A C205A Mutation：C22A C105A C205A Mutation：C22A C105A C205A Mutation：C22A C105A C205A JEI (3-{(2S,4R)-4-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2-[(2-phosphonoethoxy)methyl]pyrrolidin-1-yl}-3-oxopropyl)phosphonic acid × 4 MG MAGNESIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.3 M calcium acetate, 20% PEG 3350
Resolution 2.27 Å R-free 0.237
8TPY Structure of human hypoxanthine guanine phosphoribzosyltransferase in complex with [2S,4R] 4-Guanin-9-yl-2-hydroxymethyl-1-N-(3-phosphonopropionyl)pyrrolidine Deposited 2023-08-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–218（218 aa）
Chain B 1–218（218 aa）
Chain C 1–218（218 aa）
Chain D 1–218（218 aa）
Mutation：C22A C105A C205A Mutation：C22A C105A C205A Mutation：C22A C105A C205A Mutation：C22A C105A C205A JG6 {3-[(2S,4R)-4-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2-(hydroxymethyl)pyrrolidin-1-yl]-3-oxopropyl}phosphonic acid × 4 MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.3 M calcium acetate, 20% PEG 3350
Resolution 2.50 Å R-free 0.260

23 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HPRT_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–214； UniProt 4–217 Author chain B； PDBConstruct 1–214； UniProt 4–217

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1d6n

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d6n
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d6n
Deposition date deposition_date1999-10-14
Structure title titleTERNARY COMPLEX STRUCTURE OF HUMAN HGPRTASE, PRPP, MG2+, AND THE INHIBITOR HPP REVEALS THE INVOLVEMENT OF THE FLEXIBLE LOOP IN SUBSTRATE BINDING
Keywords keywordsHGPRTASE, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.77 Å
Radius of gyration Rg (electron density) rg_electron21.58 Å
Forward intensity I(0) i040815100.00
Molecular weight molecular_weight49074.0 kDa
Excluded volume excluded_volume61328 ų
Envelope volume envelope_volume72514 ų
Hydration-shell volume shell_volume27070 ų
Envelope diameter envelope_diameter72.3 Å
Shell Rg shell_rg29.04 Å
Envelope Rg envelope_rg21.77 Å
Shape Rg shape_rg21.59 Å
Total Rg total_rg22.43 Å
Total atoms total_atoms3438
Residues n_residues428
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax70.3 Å
Rg (real space) rg_real22.63 Å
Rg uncertainty (real space) rg_real_error0.30 Å
I(0) (real space) i0_real4.0820e+07
I(0) uncertainty (real space) i0_real_error5.0870e+05
Rg (reciprocal space) rg_reciprocal22.66 Å
I(0) (reciprocal space) i0_reciprocal40820000.0000
Solution quality estimate total_estimate0.9024
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.7 Å
Skewness Skewness skewness0.155
Kurtosis Kurtosis kurtosis-0.456
Angular range angular_range— – 0.3500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10330000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.996
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1d6na_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.61 — PRTase-like
Superfamily Superfamily superfamilyc.61.1 — PRTase-like
Family Family familyc.61.1.1 — Phosphoribosyltransferases (PRTases)
Domain ID domain_idd1d6nb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.61 — PRTase-like
Superfamily Superfamily superfamilyc.61.1 — PRTase-like
Family Family familyc.61.1.1 — Phosphoribosyltransferases (PRTases)

CATH v4.4 (2 domains)

Domain ID domain_id1d6nA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2020 —
Domain ID domain_id1d6nB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2020 —
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8. Citations (1)

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9. Files and Curves (10)