3PQR
Crystal structure of Metarhodopsin II in complex with a C-terminal peptide derived from the Galpha subunit of transducin
- PDB DOI: https://doi.org/10.2210/pdb3PQR/pdb
- Classification: SIGNALING PROTEIN
- Organism(s): Bos taurus
- Mutation(s): Yes 
- Membrane Protein: Yes  PDBTMMemProtMDmpstruc
- Deposited: 2010-11-26 Released: 2011-03-09 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.85 Å
- R-Value Free: 0.250 
- R-Value Work: 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 | |||||
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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 | |||||
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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-1 | 11 | Bos taurus | Mutation(s): 2  Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for P04695 (Bos taurus) Explore P04695  Go to UniProtKB:  P04695 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P04695 | ||||
Sequence AnnotationsExpand | |||||
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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 6 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
BOG Query on BOG | G [auth A], H [auth A] | octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N | |||
RET Query on RET | E [auth A] | RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N | |||
PLM Query on PLM | I [auth A] | PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N | |||
NAG Query on NAG | F [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
SO4 Query on SO4 | J [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
ACT Query on ACT | K [auth A], L [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4 | |||||
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ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900006 Query on PRD_900006 | D | trehalose | Oligosaccharide / Nutrient |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.85 Å
- R-Value Free: 0.250 
- R-Value Work: 0.217 
- Space Group: H 3 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 241.55 | α = 90 |
b = 241.55 | β = 90 |
c = 109.87 | 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, Database references, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary