SAXSdb — 8ddb

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

Polymerase acidic protein

Influenza A virus (A/California/04/2009(H1N1))

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 ACETATE ION × 1 6-bromo-3-hydroxy-4-oxo-1,4-dihydropyridine-2-carboxylic acid × 1 SULFATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C3W5S0_I09A0
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–177； UniProt 1–183

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	8ddb
Deposition date deposition_date	2022-06-17
Structure title title	The N-terminal domain of PA endonuclease from the influenza H1N1 viral polymerase in complex with 4-(benzyloxy)-6-bromo-3-hydroxypicolinic acid
Keywords keywords	Drug discovery, metal-binding pharmacophore, isosteres, influenza endonuclease, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex; VIRAL PROTEIN,HYDROLASE/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.

8ddb__assembly_1__model_1

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

Download this curve (.dat)

8ddb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8ddb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.24 Å
Rg (electron density)	16.07 Å
Total Rg	17.04 Å
Atom count	1518
Residues	179
Excluded volume	26811 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8ddb__assembly_1__model_1`	monomeric （1）	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 (6)

Entity 1 Entity 1 polymer

Description description	Polymerase acidic protein
Molecular weight formula_weight	22367.4 kDa
EC 编号 ec_number	3.1.-.-
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	1598

MGSGSAMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCFMYSDFGSGDPNALLEHRFEIIEGRDRIMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRSLWDSFRQSERE

Source Source

Source organism organism	Influenza A virus (A/California/04/2009(H1N1))
NCBI taxonomy ID ncbi_taxonomy_id	641501
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	6-bromo-3-hydroxy-4-oxo-1,4-dihydropyridine-2-carboxylic acid
Molecular weight formula_weight	234.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	80

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Unit-cell length a length_a	76.228 Å
Unit-cell length b length_b	76.228 Å
Unit-cell length c length_c	121.608 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 62 2 2
Space-group number int_tables_number	180
Crystal system crystal_system	hexagonal

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	58.020 Å
R factor r_factor	0.1971
R_work r_work	0.1920
R_free r_free	0.2406

The N-terminal domain of PA endonuclease from the influenza H1N1 viral polymerase in complex with 4-(benzyloxy)-6-bromo-3-hydroxypicolinic acid

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

Polymerase acidic protein

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

8ddb__assembly_1__model_1

8ddb__assembly_1__model_1 | I(q)

8ddb__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

The N-terminal domain of PA endonuclease from the influenza H1N1 viral polymerase in complex with 4-(benzyloxy)-6-bromo-3-hydroxypicolinic acid

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

Polymerase acidic protein

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

8ddb__assembly_1__model_1

8ddb__assembly_1__model_1 | I(q)

8ddb__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)