4mlp

Mammalian cryptochrome in complex with a small molecule competitor of its ubiquitin ligase

Method: X-RAY DIFFRACTION

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

Cryptochrome-2

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	N-[(2S)-3-(9H-carbazol-9-yl)-2-hydroxypropyl]-N-(furan-2-ylmethyl)methanesulfonamide × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	N-[(2S)-3-(9H-carbazol-9-yl)-2-hydroxypropyl]-N-(furan-2-ylmethyl)methanesulfonamide × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	N-[(2S)-3-(9H-carbazol-9-yl)-2-hydroxypropyl]-N-(furan-2-ylmethyl)methanesulfonamide × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	N-[(2S)-3-(9H-carbazol-9-yl)-2-hydroxypropyl]-N-(furan-2-ylmethyl)methanesulfonamide × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CRY2_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–512； UniProt 1–512 Author chain B； PDBConstruct 1–512； UniProt 1–512 Author chain C； PDBConstruct 1–512； UniProt 1–512 Author chain D； PDBConstruct 1–512； UniProt 1–512

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	4mlp
Deposition date deposition_date	2013-09-06
Structure title title	Mammalian cryptochrome in complex with a small molecule competitor of its ubiquitin ligase
Keywords keywords	photolyase homology region, transcriptional repressor, PERIOD, FBXL3, CLOCK, nucleus, TRANSCRIPTION; TRANSCRIPTION
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.

4mlp__assembly_1__model_1

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

Download this curve (.dat)

4mlp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4mlp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.35 Å
Rg (electron density)	24.22 Å
Total Rg	25.22 Å
Atom count	4043
Residues	492
Excluded volume	71866 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4mlp__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4mlp__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4mlp__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4mlp__assembly_4__model_1`	monomeric （1）	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-2
Molecular weight formula_weight	58689.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,A,B,D
Atom count atom_count	17726

MAAAAVVAATVPAQSMGADGASSVHWFRKGLRLHDNPALLAAVRGARCVRCVYILDPWFAASSSVGINRWRFLLQSLEDLDTSLRKLNSRLFVVRGQPADVFPRLFKEWGVTRLTFEYDSEPFGKERDAAIMKMAKEAGVEVVTENSHTLYDLDRIIELNGQKPPLTYKRFQALISRMELPKKPAVAVSSQQMESCRAEIQENHDDTYGVPSLEELGFPTEGLGPAVWQGGETEALARLDKHLERKAWVANYERPRMNANSLLASPTGLSPYLRFGCLSCRLFYYRLWDLYKKVKRNSTPPLSLFGQLLWREFFYTAATNNPRFDRMEGNPICIQIPWDRNPEALAKWAEGKTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRGDLWVSWESGVRVFDELLLDADFSVNAGSWMWLSCSAFFQQFFHCYCPVGFGRRTDPSGDYIRRYLPKLKGFPSRYIYEPWNAPESVQKAAKCIIGVDYPRPIVNHAETSRLNIERMKQIYQQLSRY

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-[(2S)-3-(9H-carbazol-9-yl)-2-hydroxypropyl]-N-(furan-2-ylmethyl)methanesulfonamide
Molecular weight formula_weight	398.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1554

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d4mlpa1
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	d4mlpa2
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	d4mlpb1
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	d4mlpb2
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	d4mlpc1
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	d4mlpc2
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	d4mlpd1
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	d4mlpd2
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

CATH v4.4 (12 domains)

Domain ID domain_id	4mlpA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	4mlpA02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	4mlpA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	579 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3
Homologous superfamily homologous superfamily	10 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3

Domain ID domain_id	4mlpB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	4mlpB02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	4mlpB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	579 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3
Homologous superfamily homologous superfamily	10 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3

Domain ID domain_id	4mlpC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	4mlpC02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	4mlpC03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	579 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3
Homologous superfamily homologous superfamily	10 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3

Domain ID domain_id	4mlpD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	4mlpD02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	4mlpD03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	579 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3
Homologous superfamily homologous superfamily	10 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3

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Unit-cell length a length_a	48.210 Å
Unit-cell length b length_b	93.651 Å
Unit-cell length c length_c	141.179 Å
Unit-cell angle α angle_alpha	89.94 °
Unit-cell angle β angle_beta	90.09 °
Unit-cell angle γ angle_gamma	90.25 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.943 Å
Low-resolution limit resolution_low	44.458 Å
R factor r_factor	0.1798
R_work r_work	0.1795
R_free r_free	0.2167

Mammalian cryptochrome in complex with a small molecule competitor of its ubiquitin ligase

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

Cryptochrome-2

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

4mlp__assembly_1__model_1

4mlp__assembly_1__model_1 | I(q)

4mlp__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) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Mammalian cryptochrome in complex with a small molecule competitor of its ubiquitin ligase

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

Cryptochrome-2

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

4mlp__assembly_1__model_1

4mlp__assembly_1__model_1 | I(q)

4mlp__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) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)