SAXSdb — 7c6b

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

Protein argonaute-2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	3-[3-[9-[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]purin-6-yl]phenyl]propanoic acid × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	3-[3-[9-[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]purin-6-yl]phenyl]propanoic acid × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	3-[3-[9-[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]purin-6-yl]phenyl]propanoic acid × 1 PHOSPHATE ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AGO2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–139； UniProt 440–578 Author chain B； PDBConstruct 1–139； UniProt 440–578 Author chain C； PDBConstruct 1–139； UniProt 440–578

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	7c6b
Deposition date deposition_date	2020-05-21
Structure title title	Crystal structure of Ago2 MID domain in complex with 6-(3-(2-carboxyethyl)phenyl)purine riboside monophosphate
Keywords keywords	ARGONAUTE, MID DOMAIN, RIBONUCLEOPROTEIN, RNA-BINDING, RNA-MEDIATED GENE SILENCING, TRANSLATION REGULATION, RNA BINDING PROTEIN; RNA BINDING 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.

7c6b__assembly_1__model_1

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

Download this curve (.dat)

7c6b__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7c6b__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.46 Å
Rg (electron density)	14.04 Å
Total Rg	15.18 Å
Atom count	1071
Residues	134
Excluded volume	19262 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7c6b__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7c6b__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`7c6b__assembly_3__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 (4)

Entity 1 Entity 1 polymer

Description description	Protein argonaute-2
Molecular weight formula_weight	15465.2 kDa
EC 编号 ec_number	3.1.26.-
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	3520

KQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNIL

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 non-polymer

Description description	3-[3-[9-[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]purin-6-yl]phenyl]propanoic acid
Molecular weight formula_weight	480.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	283

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d7c6ba_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.44 — Phosphotyrosine protein phosphatases I-like
Superfamily Superfamily superfamily	c.44.3 — PIWI domain N-terminal-like
Family Family family	c.44.3.0 — automated matches

Domain ID domain_id	d7c6bb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.44 — Phosphotyrosine protein phosphatases I-like
Superfamily Superfamily superfamily	c.44.3 — PIWI domain N-terminal-like
Family Family family	c.44.3.0 — automated matches

Domain ID domain_id	d7c6bc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.44 — Phosphotyrosine protein phosphatases I-like
Superfamily Superfamily superfamily	c.44.3 — PIWI domain N-terminal-like
Family Family family	c.44.3.0 — automated matches

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Unit-cell length a length_a	47.280 Å
Unit-cell length b length_b	66.460 Å
Unit-cell length c length_c	40.420 Å
Unit-cell angle α angle_alpha	107.06 °
Unit-cell angle β angle_beta	95.63 °
Unit-cell angle γ angle_gamma	86.40 °
Molecules per unit cell Z z_pdb	3

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

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	38.510 Å
R factor r_factor	0.1962
R_work r_work	0.1944
R_free r_free	0.2286

Crystal structure of Ago2 MID domain in complex with 6-(3-(2-carboxyethyl)phenyl)purine riboside monophosphate

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

Protein argonaute-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

7c6b__assembly_1__model_1

7c6b__assembly_1__model_1 | I(q)

7c6b__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

7. Citations (1)

Crystal structure of Ago2 MID domain in complex with 6-(3-(2-carboxyethyl)phenyl)purine riboside monophosphate

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

Protein argonaute-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

7c6b__assembly_1__model_1

7c6b__assembly_1__model_1 | I(q)

7c6b__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

7. Citations (1)