2Z73
Crystal structure of squid rhodopsin
- PDB DOI: https://doi.org/10.2210/pdb2Z73/pdb
- Classification: MEMBRANE PROTEIN
- Organism(s): Todarodes pacificus
- Mutation(s): No 
- Membrane Protein: Yes  OPMPDBTMMemProtMD
- Deposited: 2007-08-13 Released: 2008-05-13 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.206 
- R-Value Work: 0.188 
- R-Value Observed: 0.188 
This is version 1.4 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 | 448 | Todarodes pacificus | Mutation(s): 0  Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for P31356 (Todarodes pacificus) Explore P31356  Go to UniProtKB:  P31356 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P31356 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 6 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
PC1 Query on PC1 | N [auth B] | 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C44 H88 N O8 P NRJAVPSFFCBXDT-HUESYALOSA-N | |||
TWT Query on TWT | G [auth A], M [auth B] | DOCOSANE C22 H46 HOWGUJZVBDQJKV-UHFFFAOYSA-N | |||
BOG Query on BOG | C [auth A], H [auth B] | octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N | |||
RET Query on RET | D [auth A], J [auth B] | RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N | |||
PLM Query on PLM | E [auth A], F [auth A], K [auth B], L [auth B] | PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N | |||
SO4 Query on SO4 | I [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.206 
- R-Value Work: 0.188 
- R-Value Observed: 0.188 
- Space Group: P 62
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 122.55 | α = 90 |
b = 122.55 | β = 90 |
c = 158.74 | γ = 120 |
Software Name | Purpose |
---|---|
ADSC | data collection |
MOLREP | phasing |
CNS | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
Entry History 
Deposition Data
- Released Date: 2008-05-13  Deposition Author(s): Murakami, M., Kouyama, T.
Revision History (Full details and data files)
- Version 1.0: 2008-05-13
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2017-10-11
Changes: Data collection - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.4: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary