SAXSdb — 2way

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

ATP-DEPENDENT RNA HELICASE DDX6

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	ENHANCER OF MRNA-DECAPPING PROTEIN 3 × 1 （Q96F86） GLYCEROL × 3 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	ENHANCER OF MRNA-DECAPPING PROTEIN 3 × 1 （Q96F86） GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DDX6_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–193； UniProt 296–483 Author chain C； PDBConstruct 6–193； UniProt 296–483

ENHANCER OF MRNA-DECAPPING PROTEIN 3

HOMO SAPIENS

UniProt Q96F86

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	ATP-DEPENDENT RNA HELICASE DDX6 × 1 （P26196） GLYCEROL × 3 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	ATP-DEPENDENT RNA HELICASE DDX6 × 1 （P26196） GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EDC3_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 8–44； UniProt 192–228 Author chain D； PDBConstruct 8–44； UniProt 192–228

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	2way
Deposition date deposition_date	2009-02-18
Structure title title	Structure of the human DDX6 C-terminal domain in complex with an EDC3- FDF peptide
Keywords keywords	;DEAD-BOX PROTEIN, NUCLEOTIDE-BINDING, P54, RCK, MIRNA, P-BODIES, HELICASE, DECAPPING, RNA-BINDING, PROTO-ONCOGENE, PHOSPHOPROTEIN, CHROMOSOMAL REARRANGEMENT, ATP-DEPENDENT RNA HELICASE, HYDROLASE, CYTOPLASM, MRNA DECAY, ATP-BINDING ;; HYDROLASE
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.

2way__assembly_1__model_1

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

Download this curve (.dat)

2way__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2way__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.66 Å
Rg (electron density)	16.21 Å
Total Rg	17.27 Å
Atom count	1477
Residues	179
Excluded volume	26409 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2way__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2way__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	ATP-DEPENDENT RNA HELICASE DDX6
Molecular weight formula_weight	22475.7 kDa
EC 编号 ec_number	3.6.1.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	3087

GPQDPYEINLMEELTLKGVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLHRIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNIDKSLYVAEYHSEPVEDEKP

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	ENHANCER OF MRNA-DECAPPING PROTEIN 3
Molecular weight formula_weight	5069.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

GPHMADLFGDDIEEIPDTDFDFEGNLALFDKAAVFEEIDTYERR

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	111

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2waya_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.0 — automated matches

Domain ID domain_id	d2wayc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	2wayA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2wayC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Unit-cell length a length_a	46.920 Å
Unit-cell length b length_b	80.460 Å
Unit-cell length c length_c	110.310 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	8

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	45.500 Å
R factor r_factor	0.2140
R_work r_work	0.2100
R_free r_free	0.2750

Structure of the human DDX6 C-terminal domain in complex with an EDC3- FDF peptide

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

ATP-DEPENDENT RNA HELICASE DDX6

State in the Current Structure

Other States of the Same Protein in the Database

ENHANCER OF MRNA-DECAPPING PROTEIN 3

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

2way__assembly_1__model_1

2way__assembly_1__model_1 | I(q)

2way__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of the human DDX6 C-terminal domain in complex with an EDC3- FDF peptide

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

ATP-DEPENDENT RNA HELICASE DDX6

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ENHANCER OF MRNA-DECAPPING PROTEIN 3

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

2way__assembly_1__model_1

2way__assembly_1__model_1 | I(q)

2way__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)