1GZM
Structure of Bovine Rhodopsin in a Trigonal Crystal Form
- PDB DOI: https://doi.org/10.2210/pdb1GZM/pdb
- Classification: SIGNALING PROTEIN
- Organism(s): Bos taurus
- Mutation(s): No 
- Membrane Protein: Yes  OPMPDBTMMemProtMD
- Deposited: 2002-05-24 Released: 2003-11-20 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.65 Å
- R-Value Free: 0.235 
- R-Value Work: 0.202 
- R-Value Observed: 0.202 
This is version 2.1 of the entry. See complete history. 
Re-refinement Note
A newer entry is available that reflects an alternative modeling of the original data: 3C9L
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
RHODOPSIN | 349 | Bos taurus | Mutation(s): 0  Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for P02699 (Bos taurus) Explore P02699  Go to UniProtKB:  P02699 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P02699 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C, D, E, F | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Small Molecules
Ligands 6 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
PEF Query on PEF | J [auth A], X [auth B] | DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE C37 H74 N O8 P SLKDGVPOSSLUAI-PGUFJCEWSA-N | |||
C8E Query on C8E | AA [auth B] BA [auth B] CA [auth B] L [auth A] M [auth A] | (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C16 H34 O5 FEOZZFHAVXYAMB-UHFFFAOYSA-N | |||
RET Query on RET | G [auth A], S [auth B] | RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N | |||
PLM Query on PLM | H [auth A], I [auth A], T [auth B], U [auth B] | PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N | |||
LDA Query on LDA | DA [auth B], K [auth A], Y [auth B] | LAURYL DIMETHYLAMINE-N-OXIDE C14 H31 N O SYELZBGXAIXKHU-UHFFFAOYSA-N | |||
ZN Query on ZN | EA [auth B], R [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.65 Å
- R-Value Free: 0.235 
- R-Value Work: 0.202 
- R-Value Observed: 0.202 
- Space Group: P 31
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 103.82 | α = 90 |
b = 103.82 | β = 90 |
c = 76.59 | γ = 120 |
Software Name | Purpose |
---|---|
CNS | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
AMoRE | phasing |
Entry History 
Deposition Data
- Released Date: 2003-11-20  Deposition Author(s): Li, J.
Revision History (Full details and data files)
- Version 1.0: 2003-11-20
Type: Initial release - Version 1.1: 2011-10-19
Changes: Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance - Version 1.2: 2019-05-08
Changes: Data collection, Derived calculations, Experimental preparation, Other - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary - Version 2.1: 2023-12-13
Changes: Data collection, Database references, Refinement description, Structure summary