SAXSdb — 1dtj

▼

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

RNA-BINDING NEUROONCOLOGICAL VENTRAL ANTIGEN 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	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 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	NOVA2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–76； UniProt 378–452 Author chain B； PDBConstruct 2–76； UniProt 378–452 Author chain C； PDBConstruct 2–76； UniProt 378–452 Author chain D； PDBConstruct 2–76； UniProt 378–452

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	1dtj
Deposition date deposition_date	2000-01-12
Structure title title	CRYSTAL STRUCTURE OF NOVA-2 KH3 K-HOMOLOGY RNA-BINDING DOMAIN
Keywords keywords	KH domain, alpha-beta fold RNA-binding motif, IMMUNE SYSTEM; IMMUNE SYSTEM
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.

1dtj__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1dtj__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1dtj__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	12.35 Å
Rg (electron density)	10.79 Å
Total Rg	12.25 Å
Atom count	467
Residues	64
Excluded volume	8339 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1dtj__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1dtj__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1dtj__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1dtj__assembly_4__model_1`	monomeric （1）	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) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1dtja_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.51 — Eukaryotic type KH-domain (KH-domain type I)
Superfamily Superfamily superfamily	d.51.1 — Eukaryotic type KH-domain (KH-domain type I)
Family Family family	d.51.1.1 — Eukaryotic type KH-domain (KH-domain type I)

Domain ID domain_id	d1dtjb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.51 — Eukaryotic type KH-domain (KH-domain type I)
Superfamily Superfamily superfamily	d.51.1 — Eukaryotic type KH-domain (KH-domain type I)
Family Family family	d.51.1.1 — Eukaryotic type KH-domain (KH-domain type I)

Domain ID domain_id	d1dtjc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.51 — Eukaryotic type KH-domain (KH-domain type I)
Superfamily Superfamily superfamily	d.51.1 — Eukaryotic type KH-domain (KH-domain type I)
Family Family family	d.51.1.1 — Eukaryotic type KH-domain (KH-domain type I)

Domain ID domain_id	d1dtjd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.51 — Eukaryotic type KH-domain (KH-domain type I)
Superfamily Superfamily superfamily	d.51.1 — Eukaryotic type KH-domain (KH-domain type I)
Family Family family	d.51.1.1 — Eukaryotic type KH-domain (KH-domain type I)

CATH v4.4 (4 domains)

Domain ID domain_id	1dtjA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — K Homology domain, type 1

Domain ID domain_id	1dtjB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — K Homology domain, type 1

Domain ID domain_id	1dtjC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — K Homology domain, type 1

Domain ID domain_id	1dtjD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — K Homology domain, type 1

▶

Unit-cell length a length_a	66.500 Å
Unit-cell length b length_b	61.100 Å
Unit-cell length c length_c	97.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.20 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2290
R_work r_work	0.2250
R_free r_free	0.2790

Description description	RNA-BINDING NEUROONCOLOGICAL VENTRAL ANTIGEN 2
Molecular weight formula_weight	8288.6 kDa
Mutation mutation	I10M
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	2128

CRYSTAL STRUCTURE OF NOVA-2 KH3 K-HOMOLOGY RNA-BINDING DOMAIN

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

RNA-BINDING NEUROONCOLOGICAL VENTRAL ANTIGEN 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

1dtj__assembly_4__model_1

1dtj__assembly_4__model_1 | I(q)

1dtj__assembly_4__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	211

CRYSTAL STRUCTURE OF NOVA-2 KH3 K-HOMOLOGY RNA-BINDING DOMAIN

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

RNA-BINDING NEUROONCOLOGICAL VENTRAL ANTIGEN 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

1dtj__assembly_4__model_1

1dtj__assembly_4__model_1 | I(q)

1dtj__assembly_4__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)