SAXSdb — 7d19

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cryptochrome-1

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	N-[2-(2,4-dimethylphenyl)-4,6-dihydrothieno[3,4-c]pyrazol-3-yl]-4-(phenylcarbonyl)benzamide × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CRY1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–498； UniProt 1–496 Author chain B； PDBConstruct 3–498； UniProt 1–496

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7d19
Deposition date deposition_date	2020-09-14
Structure title title	Crystal structure of mouse Cryptochrome 1 in complex with compound TH129
Keywords keywords	Cryptochrome, CRY, CRY1, clock, CIRCADIAN CLOCK PROTEIN; CIRCADIAN CLOCK PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7d19__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7d19__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7d19__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	33.23 Å
Rg (electron density)	32.67 Å
Total Rg	33.27 Å
Atom count	7404
Residues	963
Excluded volume	131310 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7d19__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Cryptochrome-1
Molecular weight formula_weight	57371.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7539

GTMGVNAVHWFRKGLRLHDNPALKECIQGADTIRCVYILDPWFAGSSNVGINRWRFLLQCLEDLDANLRKLNSRLFVIRGQPADVFPRLFKEWNITKLSIEYDSEPFGKERDAAIKKLATEAGVEVIVRISHTLYDLDKIIELNGGQPPLTYKRFQTLVSKMEPLEMPADTITSDVIGKCMTPLSDDHDEKYGVPSLEELGFDTDGLSSAVWPGGETEALTRLERHLERKAWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKKVKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWISWEEGMKVFEELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIRRYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRG

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	N-[2-(2,4-dimethylphenyl)-4,6-dihydrothieno[3,4-c]pyrazol-3-yl]-4-(phenylcarbonyl)benzamide
Molecular weight formula_weight	453.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	135

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d7d19a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.28 — Cryptochrome/photolyase, N-terminal domain
Superfamily Superfamily superfamily	c.28.1 — Cryptochrome/photolyase, N-terminal domain
Family Family family	c.28.1.0 — automated matches

Domain ID domain_id	d7d19a2
Class class	a — All alpha proteins
Fold Fold fold	a.99 — Cryptochrome/photolyase FAD-binding domain
Superfamily Superfamily superfamily	a.99.1 — Cryptochrome/photolyase FAD-binding domain
Family Family family	a.99.1.1 — Cryptochrome/photolyase FAD-binding domain

Domain ID domain_id	d7d19b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.28 — Cryptochrome/photolyase, N-terminal domain
Superfamily Superfamily superfamily	c.28.1 — Cryptochrome/photolyase, N-terminal domain
Family Family family	c.28.1.0 — automated matches

Domain ID domain_id	d7d19b2
Class class	a — All alpha proteins
Fold Fold fold	a.99 — Cryptochrome/photolyase FAD-binding domain
Superfamily Superfamily superfamily	a.99.1 — Cryptochrome/photolyase FAD-binding domain
Family Family family	a.99.1.1 — Cryptochrome/photolyase FAD-binding domain

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Unit-cell length a length_a	81.139 Å
Unit-cell length b length_b	81.139 Å
Unit-cell length c length_c	141.780 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	trigonal

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	40.570 Å
R factor r_factor	0.1912
R_work r_work	0.1890
R_free r_free	0.2301

Crystal structure of mouse Cryptochrome 1 in complex with compound TH129

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cryptochrome-1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7d19__assembly_1__model_1

7d19__assembly_1__model_1 | I(q)

7d19__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

7. Citations (1)

Crystal structure of mouse Cryptochrome 1 in complex with compound TH129

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cryptochrome-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7d19__assembly_1__model_1

7d19__assembly_1__model_1 | I(q)

7d19__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

7. Citations (1)