9CWU | pdb_00009cwu

Crystal structure of human ribokinase in complex with K+

• PDB DOI: https://doi.org/10.2210/pdb9CWU/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-07-30 Released: 2025-08-06 
• Deposition Author(s): Park, J., Akanmori, N.N.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.147 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

Literature

To be published

Park, J., Akanmori, N.N.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 70.84 kDa 
• Atom Count: 5,383 
• Modeled Residue Count: 623 
• Deposited Residue Count: 660 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribokinase	A, B	330	Homo sapiens	Mutation(s): 0  Gene Names: RBKS, RBSK EC: 2.7.1.15
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H477 (Homo sapiens) Explore Q9H477  Go to UniProtKB:  Q9H477
PHAROS:  Q9H477 GTEx:  ENSG00000171174

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K (Subject of Investigation/LOI)	E [auth A], G [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.147 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.56	α = 90
b = 70.87	β = 93.06
c = 91.12	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
pointless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-06 
Deposition Author(s): Park, J., Akanmori, N.N.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-2020-04281

Revision History  

• Version 1.0: 2025-08-06
  Type: Initial release