SAXSdb — 6npi

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

Epstein-Barr nuclear antigen 1

Epstein-Barr virus (strain B95-8)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	2-pyrrol-1-ylbenzoic acid × 1 ({2-[(4-bromo-5-methyl-1,2-oxazol-3-yl)amino]-2-oxoethyl}sulfanyl)acetic acid × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EBNA1_EBVB9
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–141； UniProt 471–607 Author chain B； PDBConstruct 5–141； UniProt 471–607

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	6npi
Deposition date deposition_date	2019-01-17
Structure title title	Crystal structure of Epstein-Barr Virus Nuclear Antigen-1, EBNA1, bound to fragments
Keywords keywords	EBNA1, DNA binding protein, Epstein-Barr Virus, viral protein, viral protein-inhibitor complex; viral protein/inhibitor
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.

6npi__assembly_1__model_1

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

Download this curve (.dat)

6npi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6npi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.19 Å
Rg (electron density)	18.90 Å
Total Rg	19.86 Å
Atom count	4255
Residues	274
Excluded volume	38094 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6npi__assembly_1__model_1`	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 (4)

Entity 1 Entity 1 polymer

Description description	Epstein-Barr nuclear antigen 1
Molecular weight formula_weight	15306.7 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	4879

SHMGQGGSNPKFENIAEGLRALLARSHVERTTDEGTWVAGVFVYGGSKTSLYNLRRGTALAIPQCRLTPLSRLPFGMAPGPGPQPGPLRESIVCYFMVFLQTHIFAEVLKDAIKDLVMTKPAPTCNIRVTVCSFDDGVDLP

Source Source

Source organism organism	Epstein-Barr virus (strain B95-8)
Common name common_name	HHV-4
NCBI taxonomy ID ncbi_taxonomy_id	10377
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2-pyrrol-1-ylbenzoic acid
Molecular weight formula_weight	187.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	({2-[(4-bromo-5-methyl-1,2-oxazol-3-yl)amino]-2-oxoethyl}sulfanyl)acetic acid
Molecular weight formula_weight	309.1 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	372

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d6npia1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.8 — Viral DNA-binding domain
Family Family family	d.58.8.1 — Viral DNA-binding domain

Domain ID domain_id	d6npia2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6npib_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.8 — Viral DNA-binding domain
Family Family family	d.58.8.1 — Viral DNA-binding domain

CATH v4.4 (2 domains)

Domain ID domain_id	6npiA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	390 — Epstein Barr virus nuclear antigen-1, DNA-binding domain

Domain ID domain_id	6npiB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	390 — Epstein Barr virus nuclear antigen-1, DNA-binding domain

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Unit-cell length a length_a	59.704 Å
Unit-cell length b length_b	67.452 Å
Unit-cell length c length_c	69.498 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.501 Å
Low-resolution limit resolution_low	30.342 Å
R factor r_factor	0.1421
R_work r_work	0.1410
R_free r_free	0.1626

Crystal structure of Epstein-Barr Virus Nuclear Antigen-1, EBNA1, bound to fragments

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

Epstein-Barr nuclear antigen 1

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

6npi__assembly_1__model_1

6npi__assembly_1__model_1 | I(q)

6npi__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of Epstein-Barr Virus Nuclear Antigen-1, EBNA1, bound to fragments

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

Epstein-Barr nuclear antigen 1

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

6npi__assembly_1__model_1

6npi__assembly_1__model_1 | I(q)

6npi__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)