8YL3

Crystal Structure of Human Rab23 in Complex with GDP

• PDB DOI: https://doi.org/10.2210/pdb8YL3/pdb

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


• Deposited: 2024-03-05 Released: 2024-12-04 
• Deposition Author(s): Chau, Y.Y., Aik, W.S.
• Funding Organization(s): Other private

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.189 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 

Starting Model: experimental

Literature

Structural basis for Rab23 activation and a loss-of-function mutation in Carpenter Syndrome

Chau, Y.Y., Liang, H., Tung, W.L., Hor, C.H.H., Aik, W.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 19.56 kDa 
• Atom Count: 1,623 
• Modelled Residue Count: 164 
• Deposited Residue Count: 167 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-23	A	167	Homo sapiens	Mutation(s): 0  Gene Names: RAB23, HSPC137
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULC3 (Homo sapiens) Explore Q9ULC3  Go to UniProtKB:  Q9ULC3
PHAROS:  Q9ULC3 GTEx:  ENSG00000112210

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP (Subject of Investigation/LOI)	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.189 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.911	α = 90
b = 57.154	β = 90
c = 63.007	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-04 
Deposition Author(s): Chau, Y.Y., Aik, W.S.

---

Funding Organization	Location	Grant Number
Other private	Hong Kong	HKBU Faculty of Science Seed Money

Revision History  

• Version 1.0: 2024-12-04
  Type: Initial release