3F8A

Crystal Structure of the R132K:R111L:L121E:R59W Mutant of Cellular Retinoic Acid-Binding Protein Type II Complexed with C15-aldehyde (a retinal analog) at 1.95 Angstrom resolution.

PDB DOI: https://doi.org/10.2210/pdb3F8A/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2008-11-12 Released: 2009-11-10
Deposition Author(s): Jia, X., Geiger, J.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.246
R-Value Work: 0.204
R-Value Observed: 0.206

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Probing Wavelength Regulation with an Engineered Rhodopsin Mimic and a C15-Retinal Analogue

Lee, K.S., Berbasova, T., Vasileiou, C., Jia, X., Wang, W., Choi, Y., Nossoni, F., Geiger, J.H., Borhan, B.

(2012) Chempluschem 77: 273-276

Macromolecule Content

Total Structure Weight: 16.04 kDa
Atom Count: 1,320
Modelled Residue Count: 137
Deposited Residue Count: 137
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellular retinoic acid-binding protein 2	A	137	Homo sapiens	Mutation(s): 4 Gene Names: CRABP2
UniProt & NIH Common Fund Data Resources
Find proteins for P29373 (Homo sapiens) Explore P29373 Go to UniProtKB: P29373
PHAROS: P29373 GTEx: ENSG00000143320
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P29373
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B3P Query on B3P Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₁₁ H₂₆ N₂ O₆ HHKZCCWKTZRCCL-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
LSR Query on LSR Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	1,3,3-trimethyl-2-[(1E,3E)-3-methylpenta-1,3-dien-1-yl]cyclohexene C₁₅ H₂₄ KUEVAPFABUUVHS-AYCKBHPDSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.246
R-Value Work: 0.204
R-Value Observed: 0.206
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.468	α = 90
b = 58.468	β = 90
c = 104.031	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-11-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-11-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2014-10-01
Changes: Database references
Version 1.3: 2016-12-28
Changes: Structure summary
Version 1.4: 2021-10-20
Changes: Database references, Derived calculations
Version 1.5: 2023-09-06
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.