2I35
Crystal structure of rhombohedral crystal form of ground-state rhodopsin
- PDB DOI: https://doi.org/10.2210/pdb2I35/pdb
- Classification: MEMBRANE PROTEIN
- Organism(s): Bos taurus
- Mutation(s): No 
- Membrane Protein: Yes  PDBTMMemProtMDmpstruc
- Deposited: 2006-08-17 Released: 2006-10-17 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.80 Å
- R-Value Free: 0.418 
- R-Value Work: 0.373 
- R-Value Observed: 0.375 
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 | 349 | 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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Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
RET Query on RET | D [auth A] | RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N | |||
PLM Query on PLM | E [auth A], F [auth A] | PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.80 Å
- R-Value Free: 0.418 
- R-Value Work: 0.373 
- R-Value Observed: 0.375 
- Space Group: H 3 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 277.534 | α = 90 |
b = 277.534 | β = 90 |
c = 66.321 | γ = 120 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
MOLREP | phasing |
Entry History 
Deposition Data
- Released Date: 2006-10-17  Deposition Author(s): Stenkamp, R.E., Le Trong, I., Lodowski, D.T., Salom, D., Palczewski, K.
Revision History (Full details and data files)
- Version 1.0: 2006-10-17
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.3: 2017-10-18
Changes: Refinement description - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary