3AYM

Crystal structure of the batho intermediate of squid rhodopsin

Structural Biology Knowledgebase: 3AYM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.345
  • R-Value Work: 0.295

Literature

Macromolecules
Sequence Display for 3AYM

Classification: SIGNALING PROTEIN

Total Structure Weight: 102042.55

Macromolecule Entities
Molecule Chains Length Organism Details
Rhodopsin A, B 448 Todarodes pacificus Gene Name(s): RHO Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: G Protein-Coupled Receptors (GPCRs)

Protein Name: Rhodopsin, Squid


Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PC1
Query on PC1

B 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3-SN-PHOSPHATIDYLCHOLINE (Synonym)
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BOG
Query on BOG

A, B B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
RET
Query on RET

A, B RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PLM
Query on PLM

A PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.345
  • R-Value Work: 0.295
  • Space Group: P 62
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 122.36 α = 90.00
b = 122.36 β = 90.00
c = 158.22 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-05-09
  • Released Date: 2011-08-17
  • Deposition author(s): Murakami, M., Kouyama, T.

Revision History

  • 2011-10-26
    Type: Citation | Details: Citation update