4J4Q
Crystal structure of active conformation of GPCR opsin stabilized by octylglucoside
- PDB DOI: https://doi.org/10.2210/pdb4J4Q/pdb
- Classification: SIGNALING PROTEIN
- Organism(s): Bos taurus
- Mutation(s): Yes 
- Membrane Protein: Yes  PDBTMMemProtMD
- Deposited: 2013-02-07 Released: 2013-10-30 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.65 Å
- R-Value Free: 0.230 
- R-Value Work: 0.217 
- R-Value Observed: 0.218 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Rhodopsin | 348 | Bos taurus | Mutation(s): 0  Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for P02699 (Bos taurus) Explore P02699  Go to UniProtKB:  P02699 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P02699 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Guanine nucleotide-binding protein G(t) subunit alpha-1 | 11 | Bos taurus | Mutation(s): 2  Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for P04695 (Bos taurus) Explore P04695  Go to UniProtKB:  P04695 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P04695 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD |
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
BOG Query on BOG | E [auth A], F [auth A], G [auth A], H [auth A] | octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N | |||
PLM Query on PLM | I [auth A] | PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N | |||
SO4 Query on SO4 | J [auth A], L [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
ACT Query on ACT | K [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900006 Query on PRD_900006 | D | trehalose | Oligosaccharide / Nutrient |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.65 Å
- R-Value Free: 0.230 
- R-Value Work: 0.217 
- R-Value Observed: 0.218 
- Space Group: H 3 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 241.265 | α = 90 |
b = 241.265 | β = 90 |
c = 109.561 | γ = 120 |
Software Name | Purpose |
---|---|
MAR345dtb | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
Entry History 
Deposition Data
- Released Date: 2013-10-30  Deposition Author(s): Park, J.H., Morizumi, T., Li, Y., Hong, J.E., Pai, E.F., Hofmann, K.P., Choe, H.W., Ernst, O.P.
Revision History (Full details and data files)
- Version 1.0: 2013-10-30
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary