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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.222 (Depositor), 0.229 (DCC)
R-Value Work:
0.187 (Depositor), 0.194 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Interactom of cellular retinol binding protein 3.

Golczak, M.

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P82980
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1ALJ (Subject of Investigation/LOI) Query on A1ALJ Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1-[11-(dipyrrometheneboron difluoride)undecanoyl]-rac-glycerol C₂₇ H₄₁ B F₂ N₂ O₄ MYLJZUQNPWUJDF-QHCPKHFHSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.222 (Depositor), 0.229 (DCC)
R-Value Work: 0.187 (Depositor), 0.194 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-04-17

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.