8tpy

Structure of human hypoxanthine guanine phosphoribzosyltransferase in complex with [2S,4R] 4-Guanin-9-yl-2-hydroxymethyl-1-N-(3-phosphonopropionyl)pyrrolidine

Method: X-RAY DIFFRACTION D_max: 82.4 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Hypoxanthine-guanine phosphoribosyltransferase

Homo sapiens

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–218 Chain B； UniProt 1–218 Chain C； UniProt 1–218 Chain D； UniProt 1–218	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

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 8TPY	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
1D6N TERNARY COMPLEX STRUCTURE OF HUMAN HGPRTASE, PRPP, MG2+, AND THE INHIBITOR HPP REVEALS THE INVOLVEMENT OF THE FLEXIBLE LOOP IN SUBSTRATE BINDING Deposited 1999-10-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 4–217（214 aa） Chain B 4–217（214 aa）	Mutation：K68A 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
1D6N TERNARY COMPLEX STRUCTURE OF HUMAN HGPRTASE, PRPP, MG2+, AND THE INHIBITOR HPP REVEALS THE INVOLVEMENT OF THE FLEXIBLE LOOP IN SUBSTRATE BINDING Deposited 1999-10-14	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 A 4–217（214 aa） Chain B 4–217（214 aa）	Mutation：K68A 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
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 oligomeric state 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 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 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 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 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 ligand/ion 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

23 other PDB entries and 27 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 1–218； UniProt 1–218 Author chain B； PDBConstruct 1–218； UniProt 1–218 Author chain C； PDBConstruct 1–218； UniProt 1–218 Author chain D； PDBConstruct 1–218； UniProt 1–218

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

P(r) Distance Distribution P(r) Distribution

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8tpy
Deposition date deposition_date	2023-08-06
Structure title title	Structure of human hypoxanthine guanine phosphoribzosyltransferase in complex with [2S,4R] 4-Guanin-9-yl-2-hydroxymethyl-1-N-(3-phosphonopropionyl)pyrrolidine
Keywords keywords	inhibitor, complex, purine base, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	27.70 Å
Radius of gyration Rg (electron density) rg_electron	26.41 Å
Forward intensity I(0) i0	119901000.00
Molecular weight molecular_weight	88203.0 kDa
Excluded volume excluded_volume	111340 Å³
Envelope volume envelope_volume	133250 Å³
Hydration-shell volume shell_volume	40182 Å³
Envelope diameter envelope_diameter	85.0 Å
Shell Rg shell_rg	35.35 Å
Envelope Rg envelope_rg	26.35 Å
Shape Rg shape_rg	26.39 Å
Total Rg total_rg	27.42 Å
Total atoms total_atoms	6277
Residues n_residues	776
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	82.4 Å
Rg (real space) rg_real	27.47 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	1.1990e+08
I(0) uncertainty (real space) i0_real_error	1.5390e+06
Rg (reciprocal space) rg_reciprocal	27.54 Å
I(0) (reciprocal space) i0_reciprocal	119900000.0000
Solution quality estimate total_estimate	0.8991
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.6 Å
Skewness Skewness skewness	0.117
Kurtosis Kurtosis kurtosis	-0.439
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	68600000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.920

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Hypoxanthine-guanine phosphoribosyltransferase
Molecular weight formula_weight	24516.2 kDa
EC 编号 ec_number	2.4.2.8
Mutation mutation	C22A C105A C205A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6425

MATRSPGVVISDDEPGYDLDLFAIPNHYAEDLERVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYIKALNRNSDRSIPMTVDFIRLKSYANDQSTGDIKVIGGDDLSTLTGKNVLIVEDIIDTGKTMQTLLSLVRQYNPKMVKVASLLVKRTPRSVGYKPDFVGFEIPDKFVVGYALDYNEYFRDLNHVAVISETGKAKYKA

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	{3-[(2S,4R)-4-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2-(hydroxymethyl)pyrrolidin-1-yl]-3-oxopropyl}phosphonic acid
Molecular weight formula_weight	386.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	111

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8. Citations (1)

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Unit-cell length a length_a	74.461 Å
Unit-cell length b length_b	93.420 Å
Unit-cell length c length_c	129.320 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	75.730 Å
R factor r_factor	0.2036
R_work r_work	0.1998
R_free r_free	0.2596

fit	/app/data/saxs_computation/tp/8tpy/8tpy.fit
pddf	/app/data/pr_computation/tp/8tpy/8tpy.pr.out
profile	/app/data/saxs_computation/tp/8tpy/8tpy.dat