SAXSdb — 9thj

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

Polymerase basic protein 2

Influenza A virus (A/duck/Shantou/4610/2003(H5N1))

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	;(1~{R},2~{S},4~{R},5~{S},6~{S},7~{S})-7-[[5-fluoranyl-2-(5-fluoranyl-1~{H}-pyrazolo[3,4-b]pyridin-3-yl)pyrimidin-4-yl]amino]tricyclo[3.2.2.0^{2,4}]nonane-6-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	Q2LG68_9INFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–104； UniProt 318–420 Author chain A； PDBConstruct 108–163； UniProt 428–483

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	9thj
Deposition date deposition_date	2025-12-03
Last revision last_revision	2026-01-28
Structure title title	Crystal structure of H5N1 influenza polymerase PB2 domain in complex with compound 3
Keywords keywords	TRANSFERASE, INFLUENZA POLYMERASE, CAP-BINDING INHIBITORS; TRANSFERASE
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.

9thj__assembly_1__model_1

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

Download this curve (.dat)

9thj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9thj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.50 Å
Rg (electron density)	15.27 Å
Total Rg	16.46 Å
Atom count	1286
Residues	160
Excluded volume	22861 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9thj__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 (4)

Entity 1 Entity 1 polymer

Description description	Polymerase basic protein 2
Molecular weight formula_weight	18248.2 kDa
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	1532

GRISSSFSFGGFTFKRTSGSSVKKEEEVLTGNLQTLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGRDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNFGSGLNPMHQLLRHFQKDAKVLFQNWGIEPIDNVMGMIGILPDMTPSTEMSLRGVRVSKM

Source Source

Source organism organism	Influenza A virus (A/duck/Shantou/4610/2003(H5N1))
NCBI taxonomy ID ncbi_taxonomy_id	365107
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;(1~{R},2~{S},4~{R},5~{S},6~{S},7~{S})-7-[[5-fluoranyl-2-(5-fluoranyl-1~{H}-pyrazolo[3,4-b]pyridin-3-yl)pyrimidin-4-yl]amino]tricyclo[3.2.2.0^{2,4}]nonane-6-carboxylic acid ;
Molecular weight formula_weight	412.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
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	224

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Unit-cell length a length_a	61.030 Å
Unit-cell length b length_b	61.030 Å
Unit-cell length c length_c	71.289 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	6

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	hexagonal

Resolution resolution	0.910 Å
Low-resolution limit resolution_low	30.510 Å
R factor r_factor	0.1491
R_work r_work	0.1479
R_free r_free	0.1718

Crystal structure of H5N1 influenza polymerase PB2 domain in complex with compound 3

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

Polymerase basic protein 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

9thj__assembly_1__model_1

9thj__assembly_1__model_1 | I(q)

9thj__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

7. Citations (1)

Crystal structure of H5N1 influenza polymerase PB2 domain in complex with compound 3

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

Polymerase basic protein 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

9thj__assembly_1__model_1

9thj__assembly_1__model_1 | I(q)

9thj__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

7. Citations (1)