SAXSdb — 3rij

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

SC_2cx5

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	GLYCEROL × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5SHN1_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–83； UniProt 2–84 Author chain A； PDBConstruct 94–157； UniProt 95–158 Author chain B； PDBConstruct 1–83； UniProt 2–84 Author chain B； PDBConstruct 94–157； UniProt 95–158 Author chain C； PDBConstruct 1–83； UniProt 2–84 Author chain C； PDBConstruct 94–157； UniProt 95–158 Author chain D； PDBConstruct 1–83； UniProt 2–84 Author chain D； PDBConstruct 94–157； UniProt 95–158

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	3rij
Deposition date deposition_date	2011-04-13
Structure title title	Epitope backbone grafting by computational design for improved presentation of linear epitopes on scaffold proteins
Keywords keywords	protein grafting, flexible backbone design, epitope-scaffold, HIV, immunogen design, DE NOVO PROTEIN; DE NOVO 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.

3rij__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3rij__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3rij__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	15.93 Å
Rg (electron density)	14.52 Å
Total Rg	15.75 Å
Atom count	1101
Residues	150
Excluded volume	19758 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3rij__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3rij__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3rij__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3rij__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	SC_2cx5
Molecular weight formula_weight	17348.7 kDa
Mutation mutation	UNP F54Y,V55G,D99A,I100A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4991

SLSPSARRVQGALETRGFGHLKVVELPASTRTAKEAAQAVGAEVGQIVKSLVYGGEKGAYLFLVSGKNRLDLGKATRLVGGPLLEADKWAVAALTGFDAGGVPPVGHNTPLPAYLDEDLLGYPEVWAAGGTPRALFRATPKELLALTGAQVADLKEGLEHHHHHH

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	449

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3rija_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.116 — YbaK/ProRS associated domain
Superfamily Superfamily superfamily	d.116.1 — YbaK/ProRS associated domain
Family Family family	d.116.1.0 — automated matches

Domain ID domain_id	d3rijb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.116 — YbaK/ProRS associated domain
Superfamily Superfamily superfamily	d.116.1 — YbaK/ProRS associated domain
Family Family family	d.116.1.0 — automated matches

Domain ID domain_id	d3rijc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.116 — YbaK/ProRS associated domain
Superfamily Superfamily superfamily	d.116.1 — YbaK/ProRS associated domain
Family Family family	d.116.1.0 — automated matches

Domain ID domain_id	d3rijd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.116 — YbaK/ProRS associated domain
Superfamily Superfamily superfamily	d.116.1 — YbaK/ProRS associated domain
Family Family family	d.116.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	3rijA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	960 — YbaK protein
Homologous superfamily homologous superfamily	10 — YbaK/aminoacyl-tRNA synthetase-associated domain

Domain ID domain_id	3rijB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	960 — YbaK protein
Homologous superfamily homologous superfamily	10 — YbaK/aminoacyl-tRNA synthetase-associated domain

Domain ID domain_id	3rijC00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	960 — YbaK protein
Homologous superfamily homologous superfamily	10 — YbaK/aminoacyl-tRNA synthetase-associated domain

Domain ID domain_id	3rijD00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	960 — YbaK protein
Homologous superfamily homologous superfamily	10 — YbaK/aminoacyl-tRNA synthetase-associated domain

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Unit-cell length a length_a	70.000 Å
Unit-cell length b length_b	70.000 Å
Unit-cell length c length_c	131.400 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	16

Space group space_group	P 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	17.000 Å
R factor r_factor	—
R_work r_work	0.2523
R_free r_free	0.2938

Epitope backbone grafting by computational design for improved presentation of linear epitopes on scaffold proteins

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

SC_2cx5

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

3rij__assembly_3__model_1

3rij__assembly_3__model_1 | I(q)

3rij__assembly_3__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Epitope backbone grafting by computational design for improved presentation of linear epitopes on scaffold proteins

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

SC_2cx5

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

3rij__assembly_3__model_1

3rij__assembly_3__model_1 | I(q)

3rij__assembly_3__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)