3PXO
Crystal structure of Metarhodopsin II
- PDB DOI: https://doi.org/10.2210/pdb3PXO/pdb
- Classification: SIGNALING PROTEIN
- Organism(s): Bos taurus
- Mutation(s): No
- Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc
- Deposited: 2010-12-10 Released: 2011-03-09
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.00 Å
- R-Value Free: 0.245
- R-Value Work: 0.216
- R-Value Observed: 0.217
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 | 348 | 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 | |||||
| |||||
Oligosaccharides
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| 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 | B | 4 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD | |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| BOG Query on BOG | D [auth A], E [auth A] | octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N |  | ||
| RET Query on RET | G [auth A] | RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N |  | ||
| PLM Query on PLM | F [auth A] | PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.00 Å
- R-Value Free: 0.245
- R-Value Work: 0.216
- R-Value Observed: 0.217
- Space Group: H 3 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 241.82 | α = 90 |
| b = 241.82 | β = 90 |
| c = 111.8 | γ = 120 |
| Software Name | Purpose |
|---|---|
| MAR345dtb | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| XDS | data reduction |
| SCALA | data scaling |
Entry History
Deposition Data
- Released Date: 2011-03-09 Deposition Author(s): Choe, H.-W., Kim, Y.J., Park, J.H., Morizumi, T., Pai, E.F., Krauss, N., Hofmann, K.P., Scheerer, P., Ernst, O.P.
Revision History (Full details and data files)
- Version 1.0: 2011-03-09
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary
