8YQ0 | pdb_00008yq0

Crystal structure of human phosphoribosyl pyrophosphate synthetase 1(PRPS1) chimera swapped with three residues from PRPS2

• PDB DOI: https://doi.org/10.2210/pdb8YQ0/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-18 Released: 2025-03-19 
• Deposition Author(s): Zhang, L., Zhang, L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.250 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

Crystal structure of human phosphoribosyl pyrophosphate synthetase 1(PRPS1) chimera swapped with three residues from PRPS2

Zhang, L., Zhang, L.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 632.86 kDa 
• Atom Count: 42,231 
• Modelled Residue Count: 5,533 
• Deposited Residue Count: 5,778 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribose-phosphate pyrophosphokinase 1	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	321	Homo sapiens	Mutation(s): 0  Gene Names: PRPS1 EC: 2.7.6.1
UniProt & NIH Common Fund Data Resources
Find proteins for P60891 (Homo sapiens) Explore P60891  Go to UniProtKB:  P60891
PHAROS:  P60891 GTEx:  ENSG00000147224

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HSX (Subject of Investigation/LOI)	S [auth B], T [auth F], U [auth O]	5-O-phosphono-alpha-D-ribofuranose C5 H11 O8 P KTVPXOYAKDPRHY-AIHAYLRMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.250 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.083	α = 90
b = 108.083	β = 90
c = 659.674	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
HKL-3000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-19 
Deposition Author(s): Zhang, L., Zhang, L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22077081

Revision History  

• Version 1.0: 2025-03-19
  Type: Initial release