SAXSdb — 7tux

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

Hypoxanthine-guanine-xanthine phosphoribosyltransferase

Plasmodium falciparum

UniProt P20035

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–231	Not recorded	YBM [(3S)-3-{[(2-amino-4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}-4-hydroxybutyl]phosphonic acid × 1 POP PYROPHOSPHATE 2- × 1 MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 9 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295 K；200 mM Lithium Acetate, 20% PEG3350	Resolution 1.62 Å R-free 0.195
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–231	Not recorded	YBM [(3S)-3-{[(2-amino-4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}-4-hydroxybutyl]phosphonic acid × 1 POP PYROPHOSPHATE 2- × 1 MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 12 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295 K；200 mM Lithium Acetate, 20% PEG3350	Resolution 1.62 Å R-free 0.195
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1–231	Not recorded	YBM [(3S)-3-{[(2-amino-4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}-4-hydroxybutyl]phosphonic acid × 1 POP PYROPHOSPHATE 2- × 1 MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 10 ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295 K；200 mM Lithium Acetate, 20% PEG3350	Resolution 1.62 Å R-free 0.195
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 1–231	Not recorded	YBM [(3S)-3-{[(2-amino-4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}-4-hydroxybutyl]phosphonic acid × 1 POP PYROPHOSPHATE 2- × 1 MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 5 ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295 K；200 mM Lithium Acetate, 20% PEG3350	Resolution 1.62 Å R-free 0.195

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 7TUX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CJB MALARIAL PURINE PHOSPHORIBOSYLTRANSFERASE Deposited 1999-04-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–231（231 aa） Chain B 1–231（231 aa）	Not recorded	MG MAGNESIUM ION × 8 IRP (1S)-1(9-DEAZAHYPOXANTHIN-9YL)1,4-DIDEOXY-1,4-IMINO-D-RIBITOL-5-PHOSPHATE × 4 POP PYROPHOSPHATE 2- × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.00 Å R-free 0.239
1CJB MALARIAL PURINE PHOSPHORIBOSYLTRANSFERASE Deposited 1999-04-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain C 1–231（231 aa） Chain D 1–221（221 aa）	Not recorded	MG MAGNESIUM ION × 8 IRP (1S)-1(9-DEAZAHYPOXANTHIN-9YL)1,4-DIDEOXY-1,4-IMINO-D-RIBITOL-5-PHOSPHATE × 4 POP PYROPHOSPHATE 2- × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.00 Å R-free 0.239
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 1–56（56 aa） Fragment：RESIDUES 1-56,49-160,171-231 Chain A 171–231（61 aa） Fragment：RESIDUES 1-56,49-160,171-231 Chain B 1–56（56 aa） Fragment：RESIDUES 1-56,49-160,171-231 Chain B 171–231（61 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
3OZF Crystal Structure of Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase in complex with hypoxanthine Deposited 2010-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–231（231 aa） Chain B 1–231（231 aa） Chain C 1–231（231 aa） Chain D 1–231（231 aa）	Not recorded	HPA HYPOXANTHINE × 4 POP PYROPHOSPHATE 2- × 4 PO4 PHOSPHATE ION × 4 MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；291 K；200mM sodium citrate, 20% PEG3350, pH 7.4, vapor diffusion, sitting drop, temperature 291K	Resolution 1.94 Å R-free 0.237
3OZG Crystal Structure of Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase in complex with S-SerMe-ImmH phosphonate Deposited 2010-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–231（231 aa） Chain B 1–231（231 aa）	Not recorded	SSI [(3S)-4-hydroxy-3-{[(4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}butyl]phosphonic acid × 4 POP PYROPHOSPHATE 2- × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；291 K；200mM sodium citrate, 20% PEG3350, pH 7.4, vapor diffusion, sitting drop, temperature 291K	Resolution 1.99 Å R-free 0.264
3OZG Crystal Structure of Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase in complex with S-SerMe-ImmH phosphonate Deposited 2010-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain C 1–231（231 aa） Chain D 1–231（231 aa）	Not recorded	SSI [(3S)-4-hydroxy-3-{[(4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}butyl]phosphonic acid × 4 POP PYROPHOSPHATE 2- × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；291 K；200mM sodium citrate, 20% PEG3350, pH 7.4, vapor diffusion, sitting drop, temperature 291K	Resolution 1.99 Å R-free 0.264

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HGXR_PLAFG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–250； UniProt 1–231 Author chain B； PDBConstruct 20–250； UniProt 1–231 Author chain C； PDBConstruct 20–250； UniProt 1–231 Author chain D； PDBConstruct 20–250； UniProt 1–231

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7tux
Deposition date deposition_date	2022-02-03
Structure title title	Crystal Structure of Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase in complex with [(3S)-4-Hydroxy-3-[({2-amino-4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl}methyl)amino]butyl]phosphonic acid
Keywords keywords	;inhibitors, drug design, transferase-inhibitor complex, Malaria, transition state analogs, transferase, Plasmodium falciparum, TRANSFERASE-TRANSFERASE INHIBITOR complex ;; TRANSFERASE/TRANSFERASE INHIBITOR
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	33.51 Å
Radius of gyration Rg (electron density) rg_electron	32.98 Å
Forward intensity I(0) i0	178048000.00
Molecular weight molecular_weight	109630.0 kDa
Excluded volume excluded_volume	138380 Å³
Envelope volume envelope_volume	172230 Å³
Hydration-shell volume shell_volume	44046 Å³
Envelope diameter envelope_diameter	119.9 Å
Shell Rg shell_rg	39.20 Å
Envelope Rg envelope_rg	32.89 Å
Shape Rg shape_rg	32.99 Å
Total Rg total_rg	33.43 Å
Total atoms total_atoms	7701
Residues n_residues	922
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	109.7 Å
Rg (real space) rg_real	33.53 Å
Rg uncertainty (real space) rg_real_error	0.82 Å
I(0) (real space) i0_real	1.7800e+08
I(0) uncertainty (real space) i0_real_error	2.5860e+06
Rg (reciprocal space) rg_reciprocal	33.52 Å
I(0) (reciprocal space) i0_reciprocal	178000000.0000
Solution quality estimate total_estimate	0.8878
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	39.7 Å
Skewness Skewness skewness	0.359
Kurtosis Kurtosis kurtosis	-0.329
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	55730000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.860

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Hypoxanthine-guanine-xanthine phosphoribosyltransferase
Molecular weight formula_weight	28410.7 kDa
EC 编号 ec_number	2.4.2.22,2.4.2.8
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	8671

MGGSHHHHHHGGLVPRGSHMPIPNNPGAGENAFDPVFVNDDDGYDLDSFMIPAHYKKYLTKVLVPNGVIKNRIEKLAYDIKKVYNNEEFHILCLLKGSRGFFTALLKHLSRIHNYSAVETSKPLFGEHYVRVKSYCNDQSTGTLEIVSEDLSCLKGKHVLIVEDIIDTGKTLVKFCEYLKKFEIKTVAIACLFIKRTPLWNGFKADFVGFSIPDHFVVGYSLDYNEIFRDLDHCCLVNDEGKKKYKATSL

来源 Source

来源生物 organism	Plasmodium falciparum
通用名 common_name	malaria parasite P. falciparum
NCBI Class编号 ncbi_taxonomy_id	5833
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	[(3S)-3-{[(2-amino-4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}-4-hydroxybutyl]phosphonic acid
Molecular weight formula_weight	331.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	PYROPHOSPHATE 2-
Molecular weight formula_weight	176.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	36

Entity 6 Entity 6 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	771

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8. Citations (1)

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Unit-cell length a length_a	105.437 Å
Unit-cell length b length_b	111.199 Å
Unit-cell length c length_c	173.652 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	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.620 Å
Low-resolution limit resolution_low	57.470 Å
R factor r_factor	0.1708
R_work r_work	0.1696
R_free r_free	0.1947

fit	/app/data/saxs_computation/tu/7tux/7tux.fit
pddf	/app/data/pr_computation/tu/7tux/7tux.pr.out
profile	/app/data/saxs_computation/tu/7tux/7tux.dat

Crystal Structure of Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase in complex with [(3S)-4-Hydroxy-3-[({2-amino-4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl}methyl)amino]butyl]phosphonic acid

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

Hypoxanthine-guanine-xanthine phosphoribosyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction