6FKB

Crystal structure of N2C/D282C stabilized opsin bound to RS13

• PDB DOI: https://doi.org/10.2210/pdb6FKB/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Bos taurus
• Expression System: Homo sapiens
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMmpstruc


• Deposited: 2018-01-23 Released: 2018-04-04 
• Deposition Author(s): Mattle, D., Standfuss, J., Dawson, R.
• Funding Organization(s): Roche

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.03 Å
• R-Value Free: 0.272 
• R-Value Work: 0.258 
• R-Value Observed: 0.258 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40.1 kDa 
• Atom Count: 2,808 
• Modelled Residue Count: 329 
• Deposited Residue Count: 329 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhodopsin	A	329	Bos taurus	Mutation(s): 1  Gene Names: RHO Membrane Entity: Yes
UniProt
Find proteins for P02699 (Bos taurus) Explore P02699  Go to UniProtKB:  P02699

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DLH	M [auth A]	2-(4-chlorophenyl)-1-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-ethanone C19 H18 Cl N O3 FYEGABNDKDAYPJ-UHFFFAOYSA-N
BOG	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
PLM	B [auth A]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
NAG	C [auth A], D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN	F [auth A], G [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BMA	E [auth A]	beta-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.03 Å
• R-Value Free: 0.272 
• R-Value Work: 0.258 
• R-Value Observed: 0.258 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 242.852	α = 90
b = 242.852	β = 90
c = 111.469	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-04-04 
Deposition Author(s): Mattle, D., Standfuss, J., Dawson, R.

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Funding Organization	Location	Grant Number
Roche	Switzerland	RPF

Revision History  

• Version 1.0: 2018-04-04
  Type: Initial release
  
• Version 1.1: 2018-04-11
  Changes: Data collection, Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary