2ZIY

Crystal structure of squid rhodopsin

Structural Biology Knowledgebase: 2ZIY SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.330
  • R-Value Work: 0.302

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2ZIY

Classification: SIGNALING PROTEIN

Total Structure Weight: 42626.40

Macromolecule Entities
Molecule Chains Length Organism Details
Rhodopsin A 372 Todarodes pacificus Fragment: Truncation of C-terminal polypro by V8-protease, UNP residues 2-373:VAL18ILE confirmed by MS
Mutation: V18I
Gene Name(s): RHO Gene View

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: G Protein-Coupled Receptors (GPCRs)

Protein Name: Rhodopsin, Squid


Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PLM
Query on PLM

A PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
RET
Query on RET

A RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.330
  • R-Value Work: 0.302
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 84.32 α = 90.00
b = 108.75 β = 90.00
c = 142.16 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-02-27
  • Released Date: 2008-05-06
  • Deposition author(s): Miyano, M., Shimamura, T.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4