1L9H
Crystal structure of bovine rhodopsin at 2.6 angstroms RESOLUTION
- PDB DOI: https://doi.org/10.2210/pdb1L9H/pdb
- Classification: SIGNALING PROTEIN
- Organism(s): Bos taurus
- Mutation(s): No 
- Membrane Protein: Yes  PDBTMMemProtMDmpstruc
- Deposited: 2002-03-23 Released: 2002-05-15 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.225 
- R-Value Work: 0.188 
wwPDB Validation   3D Report Full Report
This is version 2.1 of the entry. See complete history. 
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 |
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G62182OO GlyCosmos:  G62182OO GlyGen:  G62182OO |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | D, F | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | E | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G48068RF GlyCosmos:  G48068RF GlyGen:  G48068RF |
Small Molecules
Ligands 6 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
BNG Query on BNG | AA [auth B] BA [auth B] G [auth A] H [auth A] I [auth A] | nonyl beta-D-glucopyranoside C15 H30 O6 QFAPUKLCALRPLH-UXXRCYHCSA-N | |||
RET Query on RET | JA [auth B], X [auth A] | RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N | |||
PLM Query on PLM | IA [auth B], KA [auth B], W [auth A], Y [auth A], Z [auth A] | PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N | |||
HG Query on HG | CA [auth B] DA [auth B] EA [auth B] L [auth A] M [auth A] | MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N | |||
HTO Query on HTO | S [auth A], T [auth A], U [auth A], V [auth A] | HEPTANE-1,2,3-TRIOL C7 H16 O3 HXYCHJFUBNTKQR-RNFRBKRXSA-N | |||
ZN Query on ZN | FA [auth B] GA [auth B] HA [auth B] O [auth A] P [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.225 
- R-Value Work: 0.188 
- Space Group: P 41
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 96.745 | α = 90 |
b = 96.745 | β = 90 |
c = 149.3 | γ = 90 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |
CNS | refinement |
Entry History 
Deposition Data
- Released Date: 2002-05-15  Deposition Author(s): Okada, T., Fujiyoshi, Y., Silow, M., Navarro, J., Landau, E.M., Shichida, Y.
Revision History (Full details and data files)
- Version 1.0: 2002-05-15
Type: Initial release - Version 1.1: 2008-04-28
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary