6FKD: N2C/D282C stabilized opsin

Crystal structure of N2C/D282C stabilized opsin bound to RS16. Determined by X-ray diffraction at 2.49 Å resolution. Released 4 Apr 2018.

Method: X-ray diffraction
Resolution: 2.49 Å
Organism: Bos taurus
Chains: 1
Atoms: 2,830
Mol. weight: 42.02 kDa
Ligands: PLM, BOG, DL2
Released: 4 Apr 2018

Explore 6FKD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6FKD contains 18 α-helices and 4 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 18 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
β-strand	9-11	3	1
α-helix	34-64	31
α-helix	66-68	3
α-helix	71-73	3
α-helix	74-85	12
α-helix	86-92	7
α-helix	93-98	6
α-helix	106-140	35
α-helix	150-168	19
α-helix	170-173	4
β-strand	178-181	4	2
β-strand	186-189	4	2
α-helix	196-198	3
α-helix	200-208	9
α-helix	209-213	5
α-helix	214-235	22
α-helix	241-276	36
α-helix	289-295	7
α-helix	298-303	6
α-helix	304-308	5
α-helix	311-321	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Rhodopsin	A	protein	349	Bos taurus	P02699 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6FKD_1 Rhodopsin (chains A)
XMCGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTL
YVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATL
GGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYI
PEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQE
SATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSCFGPIFMTIPAFFAKTSA
VYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA

Ligands and cofactors

ID	Name	Formula	Copies
PLM	Palmitic acid	C16 H32 O2	1
BOG	octyl beta-D-glucopyranoside	C14 H28 O6	5
DL2	5-chloranyl-2-(2-oxidanylidene-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-…	C18 H17 Cl N2 O4	1

Primary citation

Ligand channel in pharmacologically stabilized rhodopsin. Mattle, D., Kuhn, B., Aebi, J. et al. Proc Natl Acad Sci U S A (2018) 115:3640-3645. DOI 10.1073/pnas.1718084115 · PubMed

Other PDB entries of the same protein (UniProt P02699 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7ZBC 1.8 Å, Dark state crystal structure of bovine rhodopsin in Lipidic Cubic Phase (SACLA)
7ZBE 1.8 Å, Dark state crystal structure of bovine rhodopsin in Lipidic Cubic Phase (SwissFEL)
8A6C 1.8 Å, 1 picosecond light activated crystal structure of bovine rhodopsin in Lipidic Cubic Phase
8A6D 1.8 Å, 10 picosecond light activated crystal structure of bovine rhodopsin in Lipidic Cubic Phase
8A6E 1.8 Å, 100 picosecond light activated crystal structure of bovine rhodopsin in Lipidic Cubic…
1U19 2.2 Å, Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution
4X1H 2.29 Å, Opsin/G(alpha) peptide complex stabilized by nonyl-glucoside
5DYS 2.3 Å, Crystal Structure of T94I rhodopsin mutant
6FK6 2.36 Å, Crystal structure of N2C/D282C stabilized opsin bound to RS01
6FKC 2.46 Å, Crystal structure of N2C/D282C stabilized opsin bound to RS15
1L9H 2.6 Å, Crystal structure of bovine rhodopsin at 2.6 angstroms RESOLUTION
2G87 2.6 Å, Crystallographic model of bathorhodopsin

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