SAXSdb — 8ypz

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

Ribose-phosphate pyrophosphokinase 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 6 5-O-phosphono-alpha-D-ribofuranose × 5 GUANOSINE-5'-DIPHOSPHATE × 6 PHOSPHATE ION × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRPS1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–318； UniProt 2–318 Author chain B； PDBConstruct 2–318； UniProt 2–318 Author chain C； PDBConstruct 2–318； UniProt 2–318 Author chain D； PDBConstruct 2–318； UniProt 2–318 Author chain E； PDBConstruct 2–318； UniProt 2–318 Author chain F； PDBConstruct 2–318； UniProt 2–318

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	8ypz
Deposition date deposition_date	2024-03-18
Structure title title	Crystal strcture of human phosphoribosyl pyrophosphate synthetase 1 (PRPS1) in complex with GDP
Keywords keywords	Purine biosynthesis, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8ypz__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8ypz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8ypz__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	37.93 Å
Rg (electron density)	37.24 Å
Total Rg	37.65 Å
Atom count	14463
Residues	1835
Excluded volume	256670 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8ypz__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Ribose-phosphate pyrophosphokinase 1
Molecular weight formula_weight	34835.1 kDa
EC 编号 ec_number	2.7.6.1
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	14526

SPNIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGESVRGEDVYIVQSGCGEINDNLMELLIMINACKIASASRVTAVIPCFPYARQDKKDKSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFFDIPVDNLYAEPAVLKWIRENISEWRNCTIVSPDAGGAKRVTSIADRLNVDFALIHKERKKANEVDRMVLVGDVKDRVAILVDDMADTCGTICHAADKLLSAGATRVYAILTHGIFSGPAISRINNACFEAVVVTNTIPQEDKMKHCSKIQVIDISMILAEAIRRTHNGESVSYLFSHVPL

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
Molecular weight formula_weight	505.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	5-O-phosphono-alpha-D-ribofuranose
Molecular weight formula_weight	230.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	63

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Unit-cell length a length_a	186.876 Å
Unit-cell length b length_b	186.876 Å
Unit-cell length c length_c	160.641 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	48.700 Å
R factor r_factor	—
R_work r_work	0.2600
R_free r_free	0.3100

Crystal strcture of human phosphoribosyl pyrophosphate synthetase 1 (PRPS1) in complex with GDP

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

Ribose-phosphate pyrophosphokinase 1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8ypz__assembly_1__model_1

8ypz__assembly_1__model_1 | I(q)

8ypz__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

Crystal strcture of human phosphoribosyl pyrophosphate synthetase 1 (PRPS1) in complex with GDP

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

Ribose-phosphate pyrophosphokinase 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8ypz__assembly_1__model_1

8ypz__assembly_1__model_1 | I(q)

8ypz__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)