3CR6 | pdb_00003cr6

Crystal Structure of the R132K:R111L:A32E Mutant of Cellular Retinoic Acid Binding Protein Type II Complexed with C15-aldehyde (a retinal analog) at 1.22 Angstrom resolution.

PDB DOI: https://doi.org/10.2210/pdb3CR6/pdb

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

Deposited: 2008-04-04 Released: 2009-03-17
Deposition Author(s): Jia, X., Geiger, J.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.22 Å
R-Value Free:
0.185 (Depositor), 0.180 (DCC)
R-Value Work:
0.114 (Depositor), 0.170 (DCC)
R-Value Observed:
0.124 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Two distinctive orientations of binding determined by a single mutation in the CRABPII mutant-C15-aldehyde complexes

Jia, X., Lee, K.S., Vasileiou, C., Borhan, B., Geiger, J.H.

To be published.

Macromolecule Content

Total Structure Weight: 15.77 kDa
Atom Count: 1,493
Modeled 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): 3 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LSR Query on LSR 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]	1,3,3-trimethyl-2-[(1E,3E)-3-methylpenta-1,3-dien-1-yl]cyclohexene C₁₅ H₂₄ KUEVAPFABUUVHS-AYCKBHPDSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.22 Å
R-Value Free: 0.185 (Depositor), 0.180 (DCC)
R-Value Work: 0.114 (Depositor), 0.170 (DCC)
R-Value Observed: 0.124 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.852	α = 90
b = 46.347	β = 92.53
c = 37.324	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
SHELX	refinement
PDB_EXTRACT	data extraction
EMBL	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXL	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-03-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-03-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2016-12-28
Changes: Structure summary
Version 1.3: 2017-10-25
Changes: Refinement description
Version 1.4: 2021-10-20
Changes: Database references, Derived calculations
Version 1.5: 2023-08-30
Changes: Data collection, Refinement description
Version 1.6: 2024-11-13
Changes: Structure summary

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.