6fs7

Influenza A/California/04/2009 (pH1N1) endonuclease with I38T mutation with bound inhibitor, baloxavir acid (BXA)

Method: X-RAY DIFFRACTION

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

Polymerase acidic protein,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 Baloxavir acid × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 Baloxavir acid × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 Baloxavir acid × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 Baloxavir acid × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 Baloxavir acid × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 Baloxavir acid × 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 8–58； UniProt 1–51 Author chain A； PDBConstruct 60–193； UniProt 65–198 Author chain B； PDBConstruct 8–58； UniProt 1–51 Author chain B； PDBConstruct 60–193； UniProt 65–198 Author chain C； PDBConstruct 8–58； UniProt 1–51 Author chain C； PDBConstruct 60–193； UniProt 65–198 Author chain D； PDBConstruct 8–58； UniProt 1–51 Author chain D； PDBConstruct 60–193； UniProt 65–198 Author chain E； PDBConstruct 8–58； UniProt 1–51 Author chain E； PDBConstruct 60–193； UniProt 65–198 Author chain F； PDBConstruct 8–58； UniProt 1–51 Author chain F； PDBConstruct 60–193； UniProt 65–198

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	6fs7
Deposition date deposition_date	2018-02-19
Structure title title	Influenza A/California/04/2009 (pH1N1) endonuclease with I38T mutation with bound inhibitor, baloxavir acid (BXA)
Keywords keywords	Influenza, endonuclease, inhibitor, VIRAL PROTEIN; VIRAL PROTEIN
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.

6fs7__assembly_1__model_1

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

Download this curve (.dat)

6fs7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6fs7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.39 Å
Rg (electron density)	16.16 Å
Total Rg	17.24 Å
Atom count	1542
Residues	182
Excluded volume	27371 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6fs7__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6fs7__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6fs7__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6fs7__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`6fs7__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`6fs7__assembly_6__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 acidic protein,Polymerase acidic protein
Molecular weight formula_weight	22513.7 kDa
EC 编号 ec_number	3.1.-.-,3.1.-.-
Mutation mutation	I38T,I38T
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	9706

GMGSGMAMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAATCTHLEVCFMYSDFGSGDPNALLKHRFEIIEGRDRIMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRSLWDSFRQSERGE

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

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	12

Entity 3 Entity 3 non-polymer

Description description	Baloxavir acid
Molecular weight formula_weight	483.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	503

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d6fs7a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.1 — Restriction endonuclease-like
Family Family family	c.52.1.34 — PA N-terminal domain

Domain ID domain_id	d6fs7a2
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	d6fs7b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.1 — Restriction endonuclease-like
Family Family family	c.52.1.34 — PA N-terminal domain

Domain ID domain_id	d6fs7b2
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	d6fs7c1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.1 — Restriction endonuclease-like
Family Family family	c.52.1.34 — PA N-terminal domain

Domain ID domain_id	d6fs7c2
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	d6fs7d1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.1 — Restriction endonuclease-like
Family Family family	c.52.1.34 — PA N-terminal domain

Domain ID domain_id	d6fs7d2
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	d6fs7e1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.1 — Restriction endonuclease-like
Family Family family	c.52.1.34 — PA N-terminal domain

Domain ID domain_id	d6fs7e2
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	d6fs7f1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.1 — Restriction endonuclease-like
Family Family family	c.52.1.34 — PA N-terminal domain

Domain ID domain_id	d6fs7f2
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

CATH v4.4 (6 domains)

Domain ID domain_id	6fs7A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	91 — Restriction Endonuclease
Homologous superfamily homologous superfamily	90 — Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain

Domain ID domain_id	6fs7B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	91 — Restriction Endonuclease
Homologous superfamily homologous superfamily	90 — Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain

Domain ID domain_id	6fs7C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	91 — Restriction Endonuclease
Homologous superfamily homologous superfamily	90 — Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain

Domain ID domain_id	6fs7D00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	91 — Restriction Endonuclease
Homologous superfamily homologous superfamily	90 — Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain

Domain ID domain_id	6fs7E00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	91 — Restriction Endonuclease
Homologous superfamily homologous superfamily	90 — Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain

Domain ID domain_id	6fs7F00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	91 — Restriction Endonuclease
Homologous superfamily homologous superfamily	90 — Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain

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Unit-cell length a length_a	135.680 Å
Unit-cell length b length_b	75.560 Å
Unit-cell length c length_c	121.800 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	24

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.960 Å
Low-resolution limit resolution_low	90.637 Å
R factor r_factor	0.1890
R_work r_work	0.1879
R_free r_free	0.2114

Influenza A/California/04/2009 (pH1N1) endonuclease with I38T mutation with bound inhibitor, baloxavir acid (BXA)

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

Polymerase acidic protein,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

6fs7__assembly_1__model_1

6fs7__assembly_1__model_1 | I(q)

6fs7__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) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Influenza A/California/04/2009 (pH1N1) endonuclease with I38T mutation with bound inhibitor, baloxavir acid (BXA)

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

Polymerase acidic protein,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

6fs7__assembly_1__model_1

6fs7__assembly_1__model_1 | I(q)

6fs7__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) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

7. Citations (1)