3F8A | pdb_00003f8a

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 (Depositor), 0.262 (DCC)
R-Value Work:
0.204 (Depositor), 0.225 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3F8A

Ligand Structure Quality Assessment

This is version 1.6 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
Modeled Residue Count: 137
Deposited Residue Count: 137
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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] mmCIF 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 (Depositor), 0.262 (DCC)
R-Value Work: 0.204 (Depositor), 0.225 (DCC)
R-Value Observed: 0.206 (Depositor)

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

View more in-depth experimental data

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
Version 1.6: 2024-10-30
Changes: Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.