6KX6: Mouse Cryptochrome 1

Crystal structure of mouse Cryptochrome 1 in complex with KL101 compound. Determined by X-ray diffraction at 2.0 Å resolution. Released 1 Apr 2020.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Mus musculus
Chains: 2
Atoms: 7,754
Mol. weight: 115.5 kDa
Ligands: DYU
Released: 1 Apr 2020

Explore 6KX6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6KX6 contains 63 α-helices and 20 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: 32 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	19-25	7
β-strand	30-37	8	1
α-helix	49-67	19
β-strand	73-77	5	1
α-helix	80-90	11
β-strand	95-99	5	1
α-helix	104-120	17
β-strand	123-127	5	1
α-helix	135-141	7
α-helix	150-158	9
α-helix	161-169	9
α-helix	172-175	4
β-strand	179	1	1
α-helix	186-190	5
α-helix	191-194	4
α-helix	196-198	3
α-helix	205-208	4
α-helix	214-228	15
α-helix	241-244	4
α-helix	246-247	2
α-helix	252-257	6
α-helix	262-274	13
α-helix	284-287	4
α-helix	288-301	14
β-strand	321	1	2
α-helix	324-331	8
α-helix	338-350	13
α-helix	355-363	9
α-helix	364-368	5
β-strand	372	1	2
α-helix	374-384	11
α-helix	390-400	11
α-helix	417-422	6
α-helix	427-432	6
α-helix	434-436	3
α-helix	447-449	3
α-helix	452-457	6
β-strand	462	1	3
β-strand	466	1	3
α-helix	467-469	3
α-helix	473-491	19

Chain B: 31 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	4
α-helix	19-25	7
β-strand	30-37	8	4
α-helix	49-67	19
β-strand	73-77	5	4
α-helix	80-90	11
β-strand	95-99	5	4
α-helix	104-120	17
β-strand	123-127	5	4
α-helix	135-141	7
α-helix	150-159	10
α-helix	161-169	9
α-helix	172-175	4
β-strand	179	1	4
α-helix	186-190	5
α-helix	191-194	4
α-helix	196-198	3
α-helix	214-228	15
α-helix	242-244	3
α-helix	246-247	2
α-helix	252-257	6
α-helix	262-275	14
α-helix	284-287	4
α-helix	288-300	13
β-strand	321	1	5
α-helix	324-332	9
α-helix	338-350	13
α-helix	355-363	9
α-helix	364-368	5
β-strand	372	1	5
α-helix	374-384	11
α-helix	390-400	11
α-helix	417-422	6
α-helix	427-432	6
α-helix	434-436	3
α-helix	447-449	3
α-helix	452-457	6
β-strand	462	1	6
β-strand	466	1	6
α-helix	467-469	3
α-helix	473-489	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cryptochrome-1	A, B	protein	498	Mus musculus	P97784 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6KX6_1 Cryptochrome-1 (chains A, B)
GTMGVNAVHWFRKGLRLHDNPALKECIQGADTIRCVYILDPWFAGSSNVGINRWRFLLQC
LEDLDANLRKLNSRLFVIRGQPADVFPRLFKEWNITKLSIEYDSEPFGKERDAAIKKLAT
EAGVEVIVRISHTLYDLDKIIELNGGQPPLTYKRFQTLVSKMEPLEMPADTITSDVIGKC
MTPLSDDHDEKYGVPSLEELGFDTDGLSSAVWPGGETEALTRLERHLERKAWVANFERPR
MNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKKVKKNSSPPLSLYGQLLWREFFYT
AATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLAR
HAVACFLTRGDLWISWEEGMKVFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPVGF
GRRTDPNGDYIRRYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEASR
LNIERMKQIYQQLSRYRG

Ligands and cofactors

ID	Name	Formula	Copies
DYU	~{N}-[2-(2,4-dimethylphenyl)-4,6-dihydrothieno[3,4-c]pyrazol-3-yl]-3,4-dimethyl…	C22 H23 N3 O 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 P97784 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5T5X 1.84 Å, High resolution structure of mouse Cryptochrome 1
7D1C 1.91 Å, Crystal structure of mouse Cryptochrome 1 in complex with compound TH303
7D0M 1.95 Å, Crystal structure of mouse CRY1 with bound cryoprotectant
6KX4 2.0 Å, Crystal structure of mouse Cryptochrome 1 apo form
6KX5 2.0 Å, Crystal structure of mouse Cryptochrome 1 in complex with KL044 compound
7WVA 2.05 Å, Crystal structure of mouse Cryptochrome 1 in complex with TH401 compound
6KX7 2.1 Å, Crystal structure of mouse Cryptochrome 1 in complex with TH301 compound
6LUE 2.1 Å, Crystal structure of mouse Cryptochrome 1 in complex with compound KL201
7DLI 2.2 Å, Crystal structure of mouse CRY1 in complex with KL001 compound
7D19 2.35 Å, Crystal structure of mouse Cryptochrome 1 in complex with compound TH129
4CT0 2.45 Å, Crystal Structure of Mouse Cryptochrome1 in Complex with Period2
4K0R 2.65 Å, Crystal structure of mouse Cryptochrome 1

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