5DYS
Crystal Structure of T94I rhodopsin mutant
- PDB DOI: https://doi.org/10.2210/pdb5DYS/pdb
- Classification: SIGNALING PROTEIN
- Organism(s): Bos taurus
- Expression System: Homo sapiens
- Mutation(s): Yes 
- Membrane Protein: Yes  PDBTMMemProtMD
- Deposited: 2015-09-25 Released: 2016-08-10 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.231 
- R-Value Work: 0.219 
- R-Value Observed: 0.220 
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): 4  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)-[beta-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:  G51945PF GlyCosmos:  G51945PF GlyGen:  G51945PF |
Small Molecules
Ligands 5 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
BOG Query on BOG | F [auth A], I [auth A] | octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N | |||
RET Query on RET | C [auth A] | RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N | |||
PLM Query on PLM | G [auth A], H [auth A] | PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N | |||
SO4 Query on SO4 | J [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
ACT Query on ACT | D [auth A], E [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.231 
- R-Value Work: 0.219 
- R-Value Observed: 0.220 
- Space Group: H 3 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 242.301 | α = 90 |
b = 242.301 | β = 90 |
c = 112.055 | γ = 120 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-08-10  Deposition Author(s): Singhal, A., Guo, Y., Matkovic, M., Schertler, G., Deupi, X., Yan, E., Standfuss, J.
Funding Organization | Location | Grant Number |
---|---|---|
Switzerland | -- |
Revision History (Full details and data files)
- Version 1.0: 2016-08-10
Type: Initial release - Version 1.1: 2016-10-19
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary