1F88

CRYSTAL STRUCTURE OF BOVINE RHODOPSIN

Structural Biology Knowledgebase: 1F88 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.186

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1F88

Classification: SIGNALING PROTEIN

Total Structure Weight: 81957.30

Macromolecule Entities
Molecule Chains Length Organism Details
RHODOPSIN A, B 348 Bos taurus Gene Name(s): RHO Gene View

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: G Protein-Coupled Receptors (GPCRs)

Protein Name: Rhodopsin


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

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

A, B N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HG
Query on HG

A, B MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

B ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.186
  • Space Group: P 41

Unit Cell:

Length (Å) Angle (°)
a = 97.25 α = 90.00
b = 97.25 β = 90.00
c = 149.54 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-06-29
  • Released Date: 2000-08-04
  • Deposition author(s): Okada, T., Palczewski, K., Stenkamp, R.E., Miyano, M.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update