1GZM

STRUCTURE OF BOVINE RHODOPSIN IN A TRIGONAL CRYSTAL FORM

Structural Biology Knowledgebase: 1GZM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.201

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1GZM

Classification: SIGNALING PROTEIN

Total Structure Weight: 87936.67

Macromolecule Entities
Molecule Chains Length Organism Details
RHODOPSIN A, B 349 Bos taurus Details: DISULFIDE LINK BETWEEN A110 AND A187, AND B110 AND B187
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 8 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PEF
Query on PEF

A, B DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]- SN-GLYCEROL (Synonym)
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
C8E
Query on C8E

A, B (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
RET
Query on RET

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

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

A, B LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-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)
BMA
Query on BMA

A, B BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-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)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
ACE
Query on ACE
A, B NON-POLYMER C2 H4 O --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.201
  • Space Group: P 31
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 103.82 α = 90.00
b = 103.82 β = 90.00
c = 76.59 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-05-24
  • Released Date: 2003-11-20
  • Deposition author(s): Li, J.

Revision History

  • 2011-10-19
    Type: Version format compliance | Details: REMARK 4
  • 2011-10-19
    Type: Refinement description | Details: REMARK 3
  • 2011-10-19
    Type: Biological assembly | Details: REMARK 300,REMARK 350
  • 2011-10-19
    Type: Linkage | Details: LINK
  • 2011-10-19
    Type: Binding sites and description | Details: REMARK 800,SITE
  • 2011-10-19
    Type: Non-polymer description | Details: HETSYN,FORMUL
  • 2011-10-19
    Type: Other | Details: REMARK 525
  • 2011-10-19
    Type: Geometry validation | Details: REMARK 500