9PSX | pdb_00009psx

Q108K:K40L:T51V:T53S:R58W:Y19W:L117E mutant of hCRBPII bound to fluorophore TD-1V-3

• PDB DOI: https://doi.org/10.2210/pdb9PSX/pdb

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


• Deposited: 2025-07-27 Released: 2025-10-29 
• Deposition Author(s): Ghanbarpour, A., Bingham, C., Geiger, J.H.
• Funding Organization(s): National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 
  0.186 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Exploring the Structure-Property Relationships of Protein/Fluorophore Complex

Santos, E., Ghanbarpour, A., Chandra, I., Bingham, C., Vasileiou, C., Geiger, J.H., Borhan, B.

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: 16.01 kDa 
• Atom Count: 1,342 
• Modeled Residue Count: 133 
• Deposited Residue Count: 133 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinol-binding protein 2	A	133	Homo sapiens	Mutation(s): 0  Gene Names: RBP2, CRBP2
UniProt & NIH Common Fund Data Resources
Find proteins for P50120 (Homo sapiens) Explore P50120  Go to UniProtKB:  P50120
PHAROS:  P50120 GTEx:  ENSG00000114113

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CKW (Subject of Investigation/LOI)	B [auth A]	(2E)-3-[5-(4-methoxyphenyl)thiophen-2-yl]but-2-enal C15 H14 O2 S KAMTWDJTZDCGFP-PKNBQFBNSA-N
ACT	C [auth A], D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free:  0.186 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.541	α = 90
b = 66.45	β = 90.384
c = 63.861	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
HKL-2000	data scaling
PHASER	phasing
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Ghanbarpour, A., Bingham, C., Geiger, J.H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)	United States	--

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release