SAXSdb — 1k5j

▼

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

Nucleoplasmin Core

Xenopus laevis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 5	water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUPL_XENLA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–124； UniProt 1–124 Author chain B； PDBConstruct 1–124； UniProt 1–124 Author chain C； PDBConstruct 1–124； UniProt 1–124 Author chain D； PDBConstruct 1–124； UniProt 1–124 Author chain E； PDBConstruct 1–124； UniProt 1–124

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1k5j
Deposition date deposition_date	2001-10-10
Structure title title	The Crystal Structure of Nucleoplasmin-Core
Keywords keywords	beta-barrel, jellyroll, beta-bulge, pentamer, CHAPERONE; CHAPERONE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1k5j__assembly_1__model_1

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

Download this curve (.dat)

1k5j__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1k5j__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.45 Å
Rg (electron density)	21.08 Å
Total Rg	21.89 Å
Atom count	3480
Residues	462
Excluded volume	63089 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1k5j__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (2)

▼

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1k5ja_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.3 — Nucleoplasmin-like core domain
Family Family family	b.121.3.1 — Nucleoplasmin-like core domain

Domain ID domain_id	d1k5jb_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.3 — Nucleoplasmin-like core domain
Family Family family	b.121.3.1 — Nucleoplasmin-like core domain

Domain ID domain_id	d1k5jc_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.3 — Nucleoplasmin-like core domain
Family Family family	b.121.3.1 — Nucleoplasmin-like core domain

Domain ID domain_id	d1k5jd_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.3 — Nucleoplasmin-like core domain
Family Family family	b.121.3.1 — Nucleoplasmin-like core domain

Domain ID domain_id	d1k5je_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.3 — Nucleoplasmin-like core domain
Family Family family	b.121.3.1 — Nucleoplasmin-like core domain

CATH v4.4 (5 domains)

Domain ID domain_id	1k5jA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	340 — Nucleoplasmin core domain

Domain ID domain_id	1k5jB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	340 — Nucleoplasmin core domain

Domain ID domain_id	1k5jC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	340 — Nucleoplasmin core domain

Domain ID domain_id	1k5jD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	340 — Nucleoplasmin core domain

Domain ID domain_id	1k5jE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	340 — Nucleoplasmin core domain

▶

Unit-cell length a length_a	116.700 Å
Unit-cell length b length_b	67.100 Å
Unit-cell length c length_c	101.700 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	123.30 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	20

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2510
R_work r_work	0.2189
R_free r_free	0.2516

Description description	Nucleoplasmin Core
Molecular weight formula_weight	13752.7 kDa
Mutation mutation	D27N, N61H
Source method src_method	man
Copy count entity_count	5

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	3627

The Crystal Structure of Nucleoplasmin-Core

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

Nucleoplasmin Core

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

1k5j__assembly_1__model_1

1k5j__assembly_1__model_1 | I(q)

1k5j__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	147

The Crystal Structure of Nucleoplasmin-Core

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

Nucleoplasmin Core

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

1k5j__assembly_1__model_1

1k5j__assembly_1__model_1 | I(q)

1k5j__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)