SAXSdb — 1o6e

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

CAPSID PROTEIN P40

HUMAN HERPESVIRUS 4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	PHOSPHORYLISOPROPANE × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PPR_EBVB9
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–235； UniProt 1–235 Author chain B； PDBConstruct 1–235； UniProt 1–235

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	1o6e
Deposition date deposition_date	2002-09-13
Structure title title	Epstein-Barr virus protease
Keywords keywords	PROTEINASE, BETA-BARREL, HYDROLASE, SERINE PROTEASE, STRUCTURAL PROTEOMICS IN EUROPE, SPINE, STRUCTURAL GENOMICS; HYDROLASE
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.

1o6e__assembly_1__model_1

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

Download this curve (.dat)

1o6e__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1o6e__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.80 Å
Rg (electron density)	37.88 Å
Total Rg	38.09 Å
Atom count	6994
Residues	914
Excluded volume	124880 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1o6e__assembly_1__model_1`	tetrameric （4）	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	CAPSID PROTEIN P40
Molecular weight formula_weight	25424.0 kDa
EC 编号 ec_number	3.4.21.97
Mutation mutation	YES
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	3509

MVQAPSVYVCGFVERPDAPPKDACLHLDPLTVKSQLPLKKPLPLTVEHLPDAPVGSVFGLYQSSAGLFSAASITSGDFLSLLDSIYHDCDIAQSQRLPLPREPKVEALHAWLPSLSLASLHPDIPQTTADGGKLSFFDHVSICALGRRRGTTAVYGTDLAWVLKHFSDLEPSIAAQIENDANAAKRESGCPEDHPLPLTKLIAKAIDAGFLRNRVETLRQDRGVANIPAESYLKA

Source Source

Source organism organism	HUMAN HERPESVIRUS 4
Common name common_name	HUMAN HERPESVIRUS 4
NCBI taxonomy ID ncbi_taxonomy_id	10376
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	PHOSPHORYLISOPROPANE
Molecular weight formula_weight	140.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	12

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1o6ea_
Class class	b — All beta proteins
Fold Fold fold	b.57 — Herpes virus serine proteinase, assemblin
Superfamily Superfamily superfamily	b.57.1 — Herpes virus serine proteinase, assemblin
Family Family family	b.57.1.1 — Herpes virus serine proteinase, assemblin

Domain ID domain_id	d1o6eb_
Class class	b — All beta proteins
Fold Fold fold	b.57 — Herpes virus serine proteinase, assemblin
Superfamily Superfamily superfamily	b.57.1 — Herpes virus serine proteinase, assemblin
Family Family family	b.57.1.1 — Herpes virus serine proteinase, assemblin

CATH v4.4 (2 domains)

Domain ID domain_id	1o6eA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	16 — Serine Protease, Human Cytomegalovirus Protease; Chain A
Homologous superfamily homologous superfamily	10 — Herpesvirus/Caudovirus protease domain

Domain ID domain_id	1o6eB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	16 — Serine Protease, Human Cytomegalovirus Protease; Chain A
Homologous superfamily homologous superfamily	10 — Herpesvirus/Caudovirus protease domain

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Unit-cell length a length_a	52.800 Å
Unit-cell length b length_b	52.800 Å
Unit-cell length c length_c	330.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	42.000 Å
R factor r_factor	0.1970
R_work r_work	0.1970
R_free r_free	0.2730

Epstein-Barr virus protease

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

CAPSID PROTEIN P40

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

1o6e__assembly_1__model_1

1o6e__assembly_1__model_1 | I(q)

1o6e__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Epstein-Barr virus protease

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

CAPSID PROTEIN P40

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

1o6e__assembly_1__model_1

1o6e__assembly_1__model_1 | I(q)

1o6e__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)