SAXSdb — 3cvy

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

RE11660p

Drosophila melanogaster

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	;DNA (5'-D(DAPDCPDAPDGPDCPDGPDGPDTPDTPDGPDCPDAPDGPDGPDT)-3') ; × 1 ;DNA (5'-D(DTPDAPDCPDCPDTPDGPDCPDAPDAPDCPDCPDGPDCPDTPDG)-3') ; × 1 FLAVIN-ADENINE DINUCLEOTIDE × 1 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8SXK5_DROME
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 24–543； UniProt 1–520

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	3cvy
Deposition date deposition_date	2008-04-20
Structure title title	Drosophila melanogaster (6-4) photolyase bound to repaired ds DNA
Keywords keywords	DNA repair, Lyase-DNA COMPLEX; Lyase/DNA
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.

3cvy__assembly_1__model_1

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

Download this curve (.dat)

3cvy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cvy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.56 Å
Rg (electron density)	25.45 Å
Total Rg	26.39 Å
Atom count	4772
Residues	531
Excluded volume	83021 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cvy__assembly_1__model_1`	trimeric （3）	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 (5)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(DAPDCPDAPDGPDCPDGPDGPDTPDTPDGPDCPDAPDGPDGP*DT)-3') ;
Molecular weight formula_weight	4650.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C
Atom count atom_count	4781

ACAGCGGTTGCAGGT

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(DTPDAPDCPDCPDTPDGPDCPDAPDAPDCPDCPDGPDCPDTP*DG)-3') ;
Molecular weight formula_weight	4529.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

TACCTGCAACCGCTG

Entity 3 Entity 3 polymer

Description description	RE11660p
Molecular weight formula_weight	62910.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MASWSHPQFEKGASTSLYKKAGLMDSQRSTLVHWFRKGLRLHDNPALSHIFTAANAAPGRYFVRPIFILDPGILDWMQVGANRWRFLQQTLEDLDNQLRKLNSRLFVVRGKPAEVFPRIFKSWRVEMLTFETDIEPYSVTRDAAVQKLAKAEGVRVETHCSHTIYNPELVIAKNLGKAPITYQKFLGIVEQLKVPKVLGVPEKLKNMPTPPKDEVEQKDSAAYDCPTMKQLVKRPEELGPNKFPGGETEALRRMEESLKDEIWVARFEKPNTAPNSLEPSTTVLSPYLKFGCLSARLFNQKLKEIIKRQPKHSQPPVSLIGQLMWREFYYTVAAAEPNFDRMLGNVYCMQIPWQEHPDHLEAWTHGRTGYPFIDAIMRQLRQEGWIHHLARHAVACFLTRGDLWISWEEGQRVFEQLLLDQDWALNAGNWMWLSASAFFHQYFRVYSPVAFGKKTDPQGHYIRKYVPELSKYPAGCIYEPWKASLVDQRAYGCVLGTDYPHRIVKHEVVHKENIKRMGAAYKVNREVRTGKEEESSFEEKSET

Source Source

Source organism organism	Drosophila melanogaster
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	9

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3cvya1
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	d3cvya2
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.99.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id	3cvyA01
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	3cvyA02
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	3cvyA03
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	83.360 Å
Unit-cell length b length_b	88.840 Å
Unit-cell length c length_c	86.590 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	39.530 Å
R factor r_factor	0.2151
R_work r_work	0.2125
R_free r_free	0.2658

Drosophila melanogaster (6-4) photolyase bound to repaired ds DNA

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

RE11660p

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

3cvy__assembly_1__model_1

3cvy__assembly_1__model_1 | I(q)

3cvy__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Drosophila melanogaster (6-4) photolyase bound to repaired ds DNA

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

RE11660p

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

3cvy__assembly_1__model_1

3cvy__assembly_1__model_1 | I(q)

3cvy__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)