5EN0
Crystal Structure of T94I rhodopsin mutant
- PDB DOI: https://doi.org/10.2210/pdb5EN0/pdb
- Classification: SIGNALING PROTEIN
- Organism(s): Bos taurus
- Expression System: Homo sapiens
- Mutation(s): Yes
- Membrane Protein: Yes PDBTMMemProtMD
- Deposited: 2015-11-08 Released: 2016-08-10
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.81 Å
- R-Value Free: 0.253
- R-Value Work: 0.207
- R-Value Observed: 0.209
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 | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Guanine nucleotide-binding protein G(t) subunit alpha-3 | 11 | Bos taurus | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for P0C7Q4 (Bos taurus) Explore P0C7Q4 Go to UniProtKB: P0C7Q4 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0C7Q4 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Oligosaccharides
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-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 | 4 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD | |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| BOG Query on BOG | G [auth A], J [auth A] | octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N |  | ||
| RET Query on RET | D [auth A] | RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N |  | ||
| PLM Query on PLM | H [auth A], I [auth A] | PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N |  | ||
| SO4 Query on SO4 | K [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| ACT Query on ACT | E [auth A], F [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.81 Å
- R-Value Free: 0.253
- R-Value Work: 0.207
- R-Value Observed: 0.209
- Space Group: H 3 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 242.269 | α = 90 |
| b = 242.269 | β = 90 |
| c = 111.147 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2016-08-10 Deposition Author(s): Singhal, A., Guo, Y., Matkovic, M., Schertler, G., Deupi, X., Yan, E., Standfuss, J.
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, Source and taxonomy, Structure summary - Version 2.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
