5xbo

Lanthanoid tagging via an unnatural amino acid for protein structure characterization

Method: SOLUTION NMR

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

Polyubiquitin-B

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	UV excision repair protein RAD23 homolog A × 1 （P54725） TERBIUM(III) ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBB_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–76； UniProt 1–76

UV excision repair protein RAD23 homolog A

Homo sapiens

UniProt P54725

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Polyubiquitin-B × 1 （P0CG47） TERBIUM(III) ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RD23A_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–49； UniProt 156–204

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	5xbo
Deposition date deposition_date	2017-03-21
Structure title title	Lanthanoid tagging via an unnatural amino acid for protein structure characterization
Keywords keywords	Unnatural amino acid, Azide-alkyne cycloaddition, Pseudo-contact shift, Transient protein complex, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	SOLUTION NMR

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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.

5xbo__assembly_1__model_18

Assembly 1 · Model 18 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5xbo__assembly_1__model_18 | I(q)

100 plotted points; both axes use logarithmic scales.

5xbo__assembly_1__model_18 | P(r) · Pending

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

Rg（Guinier）	17.25 Å
Rg (electron density)	16.01 Å
Total Rg	17.35 Å
Atom count	1999
Residues	125
Excluded volume	17699 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5xbo__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	2	`5xbo__assembly_1__model_2`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	3	`5xbo__assembly_1__model_3`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	4	`5xbo__assembly_1__model_4`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	5	`5xbo__assembly_1__model_5`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	6	`5xbo__assembly_1__model_6`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	7	`5xbo__assembly_1__model_7`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	8	`5xbo__assembly_1__model_8`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	9	`5xbo__assembly_1__model_9`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	10	`5xbo__assembly_1__model_10`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	11	`5xbo__assembly_1__model_11`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	12	`5xbo__assembly_1__model_12`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	13	`5xbo__assembly_1__model_13`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	14	`5xbo__assembly_1__model_14`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	15	`5xbo__assembly_1__model_15`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	16	`5xbo__assembly_1__model_16`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	17	`5xbo__assembly_1__model_17`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	18	`5xbo__assembly_1__model_18`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	19	`5xbo__assembly_1__model_19`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	20	`5xbo__assembly_1__model_20`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	21	`5xbo__assembly_1__model_21`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	22	`5xbo__assembly_1__model_22`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	23	`5xbo__assembly_1__model_23`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	24	`5xbo__assembly_1__model_24`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	25	`5xbo__assembly_1__model_25`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	26	`5xbo__assembly_1__model_26`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	27	`5xbo__assembly_1__model_27`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	28	`5xbo__assembly_1__model_28`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	29	`5xbo__assembly_1__model_29`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	30	`5xbo__assembly_1__model_30`	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 (3)

Entity 1 Entity 1 polymer

Description description	Polyubiquitin-B
Molecular weight formula_weight	8576.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	59970

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

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	UV excision repair protein RAD23 homolog A
Molecular weight formula_weight	5496.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

TLVTGSEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTGIPG

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	TERBIUM(III) ION
Molecular weight formula_weight	158.9 kDa
Source method src_method	man
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5xboa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d5xbob_
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.2 — UBA-like
Family Family family	a.5.2.1 — UBA domain

CATH v4.4 (1 domains)

Domain ID domain_id	5xboB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

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Lanthanoid tagging via an unnatural amino acid for protein structure characterization

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

Polyubiquitin-B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

UV excision repair protein RAD23 homolog A

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

5xbo__assembly_1__model_18

5xbo__assembly_1__model_18 | I(q)

5xbo__assembly_1__model_18 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)