SAXSdb — 5ns3

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

50S ribosomal protein L5

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Homooligomer	Protein 2 RNA 2	double-stranded RNA × 2 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL5_THETH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–177； UniProt 5–181 Author chain B； PDBConstruct 1–177； UniProt 5–181

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	5ns3
Deposition date deposition_date	2017-04-25
Structure title title	Crystal structures of Cy5 cyanine fluorophores stacked onto the end of double-stranded RNA
Keywords keywords	Cy5, fluorophore, RNA; RNA
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.

5ns3__assembly_1__model_1

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

Download this curve (.dat)

5ns3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ns3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.72 Å
Rg (electron density)	22.61 Å
Total Rg	23.37 Å
Atom count	3583
Residues	337
Excluded volume	59757 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ns3__assembly_1__model_1`	tetrameric （4）	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	50S ribosomal protein L5
Molecular weight formula_weight	20475.9 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	3597

VALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGLNPNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPFR

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	274
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	double-stranded RNA
Molecular weight formula_weight	10996.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C,D

XCGCACCUGACCCCAUGCCGAACUCAGAAGUGCG

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	14

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Unit-cell length a length_a	95.043 Å
Unit-cell length b length_b	123.895 Å
Unit-cell length c length_c	51.201 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	47.521 Å
R factor r_factor	0.2530
R_work r_work	0.2519
R_free r_free	0.2745

Crystal structures of Cy5 cyanine fluorophores stacked onto the end of double-stranded RNA

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

50S ribosomal protein L5

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

5ns3__assembly_1__model_1

5ns3__assembly_1__model_1 | I(q)

5ns3__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 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Citations (1)

Crystal structures of Cy5 cyanine fluorophores stacked onto the end of double-stranded RNA

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

50S ribosomal protein L5

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

5ns3__assembly_1__model_1

5ns3__assembly_1__model_1 | I(q)

5ns3__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 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Citations (1)