3DQB
Crystal structure of the active G-protein-coupled receptor opsin in complex with a C-terminal peptide derived from the Galpha subunit of transducin
- PDB DOI: https://doi.org/10.2210/pdb3DQB/pdb
- Classification: SIGNALING PROTEIN
- Organism(s): Bos taurus
- Mutation(s): Yes 
- Membrane Protein: Yes  PDBTMMemProtMDmpstruc
- Deposited: 2008-07-09 Released: 2008-09-23 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.20 Å
- R-Value Free: 0.248 
- R-Value Work: 0.213 
- R-Value Observed: 0.215 
This is version 2.2 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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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 |
11meric peptide form Guanine nucleotide-binding protein G(t) subunit alpha-1 | 11 | N/A | Mutation(s): 1  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 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
BOG Query on BOG | E [auth A], F [auth A], G [auth A] | octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N | |||
PLM Query on PLM | H [auth A], I [auth A] | PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.20 Å
- R-Value Free: 0.248 
- R-Value Work: 0.213 
- R-Value Observed: 0.215 
- Space Group: H 3 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 238.02 | α = 90 |
b = 238.02 | β = 90 |
c = 109.132 | γ = 120 |
Software Name | Purpose |
---|---|
HKL-2000 | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
Entry History 
Deposition Data
- Released Date: 2008-09-23  Deposition Author(s): Scheerer, P., Park, J.H., Hildebrand, P.W., Kim, Y.J., Krauss, N., Choe, H.-W., Hofmann, K.P., Ernst, O.P.
Revision History (Full details and data files)
- Version 1.0: 2008-09-23
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.2: 2014-02-05
Changes: Derived calculations - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2021-11-10
Changes: Database references, Structure summary - Version 2.2: 2023-11-01
Changes: Data collection, Refinement description