3CAP
Crystal Structure of Native Opsin: the G Protein-Coupled Receptor Rhodopsin in its Ligand-free State
- PDB DOI: https://doi.org/10.2210/pdb3CAP/pdb
- Classification: SIGNALING PROTEIN
- Organism(s): Bos taurus
- Mutation(s): No 
- Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc
- Deposited: 2008-02-20 Released: 2008-06-24 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.90 Å
- R-Value Free: 0.266 
- R-Value Work: 0.229 
- R-Value Observed: 0.231 
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 | |||||
|
Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-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, E | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G31886NL GlyCosmos:  G31886NL GlyGen:  G31886NL |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
BGL Query on BGL | G [auth A] H [auth A] I [auth A] J [auth A] L [auth B] | 2-O-octyl-beta-D-glucopyranose C14 H28 O6 BVHPDIWLWHHJPD-RKQHYHRCSA-N | |||
PLM Query on PLM | K [auth A], N [auth B] | PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.90 Å
- R-Value Free: 0.266 
- R-Value Work: 0.229 
- R-Value Observed: 0.231 
- Space Group: H 3
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 242.917 | α = 90 |
b = 242.918 | β = 90 |
c = 110.42 | γ = 120 |
Software Name | Purpose |
---|---|
MAR345dtb | data collection |
CNS | refinement |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2008-06-24  Deposition Author(s): Park, J.H., Scheerer, P., Hofmann, K.P., Choe, H.-W., Ernst, O.P.
Revision History (Full details and data files)
- Version 1.0: 2008-06-24
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary