6KX8: Mouse Cryptochrome 2

Crystal structure of mouse Cryptochrome 2 in complex with TH301 compound. Determined by X-ray diffraction at 2.25 Å resolution. Released 1 Apr 2020.

Method: X-ray diffraction
Resolution: 2.25 Å
Organism: Mus musculus
Chains: 2
Atoms: 7,655
Mol. weight: 118.67 kDa
Ligands: DYX
Released: 1 Apr 2020

Explore 6KX8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6KX8 contains 67 α-helices and 18 β-strands across 2 chains. 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: 35 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	21-27	7	1
α-helix	37-43	7
β-strand	46-55	10	1
α-helix	67-85	19
β-strand	91-95	5	1
α-helix	98-109	12
β-strand	113-117	5	1
α-helix	122-137	16
β-strand	141-145	5	1
α-helix	153-159	7
α-helix	168-177	10
α-helix	179-189	11
α-helix	190-194	5
α-helix	197-199	3
α-helix	204-208	5
α-helix	209-212	4
α-helix	232-242	11
α-helix	259-262	4
α-helix	264-265	2
α-helix	270-275	6
α-helix	280-294	15
α-helix	302-305	4
α-helix	306-318	13
α-helix	334-335	2
α-helix	338	1
β-strand	339	1	2
α-helix	340	1
α-helix	342-350	9
α-helix	356-368	13
α-helix	373-381	9
α-helix	382-386	5
β-strand	390	1	2
α-helix	392-402	11
α-helix	408-418	11
α-helix	435-440	6
α-helix	445-450	6
α-helix	452-454	3
α-helix	459-462	4
α-helix	465-467	3
α-helix	470-475	6
β-strand	480	1	3
β-strand	484	1	3
α-helix	485-487	3
α-helix	491-505	15

Chain B: 32 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	21-27	7	4
α-helix	37-43	7
β-strand	46-55	10	4
α-helix	57-62	6
α-helix	67-85	19
β-strand	91-95	5	4
α-helix	98-109	12
β-strand	113-117	5	4
α-helix	122-137	16
β-strand	141-145	5	4
α-helix	153-159	7
α-helix	168-176	9
α-helix	179-189	11
α-helix	190-195	6
α-helix	197-199	3
α-helix	205-208	4
α-helix	209-212	4
α-helix	232-245	14
α-helix	260-262	3
α-helix	270-275	6
α-helix	280-294	15
α-helix	302-305	4
α-helix	306-318	13
β-strand	339	1	5
α-helix	342-349	8
α-helix	356-368	13
α-helix	373-381	9
α-helix	382-386	5
β-strand	390	1	5
α-helix	392-402	11
α-helix	408-418	11
α-helix	435-440	6
α-helix	445-450	6
α-helix	452-454	3
α-helix	459-462	4
α-helix	465-467	3
α-helix	470-475	6
β-strand	480	1	6
β-strand	484	1	6
α-helix	485-487	3
α-helix	491-503	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cryptochrome-2	A, B	protein	514	Mus musculus	Q9R194 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6KX8_1 Cryptochrome-2 (chains A, B)
GTMAAAAVVAATVPAQSMGADGASSVHWFRKGLRLHDNPALLAAVRGARCVRCVYILDPW
FAASSSVGINRWRFLLQSLEDLDTSLRKLNSRLFVVRGQPADVFPRLFKEWGVTRLTFEY
DSEPFGKERDAAIMKMAKEAGVEVVTENSHTLYDLDRIIELNGQKPPLTYKRFQALISRM
ELPKKPAVAVSSQQMESCRAEIQENHDDTYGVPSLEELGFPTEGLGPAVWQGGETEALAR
LDKHLERKAWVANYERPRMNANSLLASPTGLSPYLRFGCLSCRLFYYRLWDLYKKVKRNS
TPPLSLFGQLLWREFFYTAATNNPRFDRMEGNPICIQIPWDRNPEALAKWAEGKTGFPWI
DAIMTQLRQEGWIHHLARHAVACFLTRGDLWVSWESGVRVFDELLLDADFSVNAGSWMWL
SCSAFFQQFFHCYCPVGFGRRTDPSGDYIRRYLPKLKGFPSRYIYEPWNAPESVQKAAKC
IIGVDYPRPIVNHAETSRLNIERMKQIYQQLSRY

Ligands and cofactors

ID	Name	Formula	Copies
DYX	1-(4-chlorophenyl)-N-[2-(4-methoxyphenyl)-5,5-bis(oxidanylidene)-4,6-dihydrothi…	C24 H24 Cl N3 O4 S	2

Primary citation

Isoform-selective regulation of mammalian cryptochromes. Miller, S., Son, Y.L., Aikawa, Y. et al. Nat Chem Biol (2020) 16:676-685. DOI 10.1038/s41589-020-0505-1 · PubMed

Other PDB entries of the same protein (UniProt Q9R194 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7V8Y 1.9 Å, Crystal structure of mouse CRY2 in complex with SHP1703 compound
4MLP 1.94 Å, Mammalian cryptochrome in complex with a small molecule competitor of its ubiquitin ligase
7V8Z 1.95 Å, Crystal structure of mouse CRY2 in complex with SHP656 compound
4I6G 2.2 Å, a vertebrate cryptochrome with FAD
7EJ9 2.6 Å, Alternative crystal structure of mouse Cryptochrome 2 in complex with TH301 compound
4I6E 2.7 Å, A vertebrate cryptochrome
4I6J 2.7 Å, A ubiquitin ligase-substrate complex
4U8H 2.8 Å, Crystal Structure of Mammalian Period-Cryptochrome Complex
7D0N 2.8 Å, Crystal structure of mouse CRY2 apo form

Browse structure collections

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