9PSV | pdb_00009psv

Q108K:K40L:T51V:T53S:R58W:Y19W:L117E mutant of hCRBPII bound to fluorophore TD-1V-7

• PDB DOI: https://doi.org/10.2210/pdb9PSV/pdb

• Classification: RETINOL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-07-27 Released: 2025-10-01 
• Deposition Author(s): Ghanbarpour, A., Bingam, 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: 1.51 Å
• R-Value Free: 
  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Exploring the Structure-Property Relationships of Protein/Fluorophore Complex

Santos, E., Ghanbarpour, A., Chandra, I., Bingam, 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.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 31.78 kDa 
• Atom Count: 2,483 
• Modeled Residue Count: 266 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinol-binding protein 2	A, B	133	Homo sapiens	Mutation(s): 7  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
A1CKU (Subject of Investigation/LOI)	C [auth A], E [auth B]	(2E)-3-[5-(dimethylamino)thiophen-2-yl]but-2-enal C10 H13 N O S OHTTZWOXIMXANB-SOFGYWHQSA-N
ACT	D [auth A], F [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free:  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.259	α = 90
b = 66.723	β = 90.783
c = 63.954	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): Ghanbarpour, A., Bingam, 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: 2025-10-01
  Type: Initial release