4BEZ

Night blindness causing G90D rhodopsin in the active conformation

Structural Biology Knowledgebase: 4BEZ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.229

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4BEZ

Classification: MEMBRANE PROTEIN

Total Structure Weight: 40545.59

Macromolecule Entities
Molecule Chains Length Organism Details
RHODOPSIN A 349 Bos taurus Mutation: N2C, G90D, D282C
Gene Name(s): RHO Gene View

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: G Protein-Coupled Receptors (GPCRs)

Protein Name: Rhodopsin


Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BOG
Query on BOG

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

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

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

A BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
ACE
Query on ACE
A NON-POLYMER C2 H4 O --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.229
  • Space Group: H 3 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 242.44 α = 90.00
b = 242.44 β = 90.00
c = 110.36 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-03-12
  • Released Date: 2013-04-24
  • Deposition author(s): Singhal, A., Ostermaier, M.K., Vishnivetskiy, S.A., Panneels, V., Homan, K.T., Tesmer, J.J.G., Veprintsev, D., Deupi, X., Gurevich, V.V., Schertler, G.F.X., Standfuss, J.

Revision History

  • 2013-06-19
    Type: Citation | Details: JRNL