3C9M
Structure of a mutant bovine rhodopsin in hexagonal crystal form
- PDB DOI: https://doi.org/10.2210/pdb3C9M/pdb
- Classification: SIGNALING PROTEIN
- Organism(s): Bos taurus
- Mutation(s): Yes 
- Membrane Protein: Yes  PDBTMMemProtMD
- Deposited: 2008-02-16 Released: 2008-08-05 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.40 Å
- R-Value Free: 0.219 
- R-Value Work: 0.174 
- R-Value Observed: 0.176 
This is version 1.6 of the entry. See complete history. 
Re-refinement Note
This entry reflects an alternative modeling of the original data in: 2J4Y
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): 2  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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Small Molecules
Ligands 3 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 | |||
NAG Query on NAG | B [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
ACE Query on ACE | C [auth A] | ACETYL GROUP C2 H4 O IKHGUXGNUITLKF-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.40 Å
- R-Value Free: 0.219 
- R-Value Work: 0.174 
- R-Value Observed: 0.176 
- Space Group: P 64
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 109.3 | α = 90 |
b = 109.3 | β = 90 |
c = 77.7 | γ = 120 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
PDB_EXTRACT | data extraction |
REFMAC | refinement |
Entry History 
Deposition Data
- Released Date: 2008-08-05  Deposition Author(s): Stenkamp, R.E.
Revision History (Full details and data files)
- Version 1.0: 2008-08-05
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.2: 2011-10-05
Changes: Other - Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description - Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary - Version 1.5: 2021-10-20
Changes: Database references, Structure summary - Version 1.6: 2023-08-30
Changes: Data collection, Refinement description