3C9L

Structure of ground-state bovine rhodospin in a hexagonal crystal form

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history. 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 1GZM



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rhodopsin348Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P02699 (Bos taurus)
Explore P02699 
Go to UniProtKB:  P02699
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02699
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B, C
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEF
Query on PEF
Download Ideal Coordinates CCD File 
I [auth A]DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
C8E
Query on C8E
Download Ideal Coordinates CCD File 
K [auth A]
L [auth A]
M [auth A]
N [auth A]
O [auth A]
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A]
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
RET
Query on RET
Download Ideal Coordinates CCD File 
F [auth A]RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
PLM
Query on PLM
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]		PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
LDA
Query on LDA
Download Ideal Coordinates CCD File 
J [auth A]LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACE
Query on ACE
Download Ideal Coordinates CCD File 
E [auth A]ACETYL GROUP
C2 H4 O
IKHGUXGNUITLKF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.82α = 90
b = 103.82β = 90
c = 76.59γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2011-08-10
    Changes: Other
  • Version 1.3: 2011-10-05
    Changes: Other
  • Version 1.4: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-08-30
    Changes: Data collection, Database references, Refinement description, Structure summary