6FK7
Crystal structure of N2C/D282C stabilized opsin bound to RS06
- PDB DOI: https://doi.org/10.2210/pdb6FK7/pdb
- Classification: MEMBRANE PROTEIN
- Organism(s): Bos taurus
- Expression System: Homo sapiens
- Mutation(s): Yes
- Membrane Protein: Yes PDBTMMemProtMDmpstruc
- Deposited: 2018-01-23 Released: 2018-04-04
- Funding Organization(s): Roche
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.62 Å
- R-Value Free: 0.253
- R-Value Work: 0.236
- R-Value Observed: 0.237
This is version 3.1 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): 1 Gene Names: RHO 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 |
| alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | B | 5 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO | |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| DO5 Query on DO5 | I [auth A] | (2~{R},3~{R})-2-(4-chlorophenyl)-3-oxidanyl-1-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-butan-1-one C21 H22 Cl N O4 GYIGPNZLXGKQBD-KUHUBIRLSA-N |  | ||
| BOG Query on BOG | D [auth A], 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 | C [auth A] | PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.62 Å
- R-Value Free: 0.253
- R-Value Work: 0.236
- R-Value Observed: 0.237
- Space Group: H 3 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 243.391 | α = 90 |
| b = 243.391 | β = 90 |
| c = 111.547 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| Aimless | data scaling |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-04-04 Deposition Author(s): Mattle, D., Standfuss, J., Dawson, R.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Roche | Switzerland | RPF |
Revision History (Full details and data files)
- Version 1.0: 2018-04-04
Type: Initial release - Version 1.1: 2018-04-11
Changes: Data collection, Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 3.0: 2021-06-02
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 3.1: 2024-01-17
Changes: Advisory, Data collection, Database references, Refinement description
