9BCB | pdb_00009bcb

Crystal structure of human cellular retinol binding protein 3 in complex with C11 TopFluor MG

• PDB DOI: https://doi.org/10.2210/pdb9BCB/pdb

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


• Deposited: 2024-04-08 Released: 2024-04-17 
• Deposition Author(s): Golczak, M.
• Funding Organization(s): National Institutes of Health/National Eye Institute (NIH/NEI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.222 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Interactom of cellular retinol binding protein 3.

Golczak, M.

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 2  

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

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

Macromolecule Content 

• Total Structure Weight: 33.44 kDa 
• Atom Count: 2,747 
• Modeled Residue Count: 274 
• Deposited Residue Count: 278 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinol-binding protein 5	A, B	139	Homo sapiens	Mutation(s): 0  Gene Names: RBP5
UniProt & NIH Common Fund Data Resources
Find proteins for P82980 (Homo sapiens) Explore P82980  Go to UniProtKB:  P82980
PHAROS:  P82980 GTEx:  ENSG00000139194

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1ALJ (Subject of Investigation/LOI)	C [auth A]	1-[11-(dipyrrometheneboron difluoride)undecanoyl]-rac-glycerol C27 H41 B F2 N2 O4 MYLJZUQNPWUJDF-QHCPKHFHSA-N
GOL	D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.222 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.213	α = 90
b = 46.257	β = 92.1
c = 71.53	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
BALBES	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-17 
Deposition Author(s): Golczak, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Eye Institute (NIH/NEI)	United States	EY023948

Revision History  

• Version 1.0: 2024-04-17
  Type: Initial release