SAXSdb — 4y2a

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

3D polymerase

Coxsackievirus B3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	2,2'-[(4-chlorobenzene-1,2-diyl)bis(oxy)]bis(5-nitrobenzonitrile) × 1 SULFATE ION × 5 GLYCEROL × 4 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLG_CXB3N
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–462； UniProt 1724–2185

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	4y2a
Deposition date deposition_date	2015-02-09
Structure title title	Crystal Structure of Coxsackie Virus B3 3D polymerase in complex with GPC-N114 inhibitor
Keywords keywords	Polymerase, Picornavirus, Coxsackievirus, GPC-N114, inhibitor, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE 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.

4y2a__assembly_1__model_1

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

Download this curve (.dat)

4y2a__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4y2a__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.22 Å
Rg (electron density)	23.11 Å
Total Rg	24.00 Å
Atom count	3807
Residues	466
Excluded volume	67819 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4y2a__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 (5)

Entity 1 Entity 1 polymer

Description description	3D polymerase
Molecular weight formula_weight	53001.6 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	3844

GEIEFIESSKDAGFPVINTPSKTKLEPSVFHQVFEGNKEPAVLRSGDPRLKANFEEAIFSKYIGNVNTHVDEYMLEAVDHYAGQLATLDISTEPMKLEDAVYGTEGLEALDLTTSAGYPYVALGIKKRDILSKKTKDLTKLKECMDKYGLNLPMVTYVKDELRSIEKVAKGKSRLIEASSLNDSVAMRQTFGNLYKTFHLNPGVVTGSAVGCDPDLFWSKIPVMLDGHLIAFDYSGYDASLSPVWFACLKMLLEKLGYTHKETNYIDYLCNSHHLYRDKHYFVRGGMPSGCSGTSIFNSMINNIIIRTLMLKVYKGIDLDQFRMIAYGDDVIASYPWPIDASLLAEAGKGYGLIMTPADKGECFNEVTWTNATFLKRYFRADEQYPFLVHPVMPMKDIHESIRWTKDPKNTQDHVRSLCLLAWHNGEHEYEEFIRKIRSVPVGRCLTLPAFSTLRRKWLDSFHHHH

Source Source

Source organism organism	Coxsackievirus B3
NCBI taxonomy ID ncbi_taxonomy_id	12072
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2,2'-[(4-chlorobenzene-1,2-diyl)bis(oxy)]bis(5-nitrobenzonitrile)
Molecular weight formula_weight	436.8 kDa
Source method src_method	man
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	man
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	man
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	25

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4y2aa1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.8 — DNA/RNA polymerases
Superfamily Superfamily superfamily	e.8.1 — DNA/RNA polymerases
Family Family family	e.8.1.4 — RNA-dependent RNA-polymerase

Domain ID domain_id	d4y2aa2
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 (2 domains)

Domain ID domain_id	4y2aA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	4y2aA03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	960 — Mitochondrial Import Receptor Subunit Tom20; Chain A
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	74.740 Å
Unit-cell length b length_b	74.740 Å
Unit-cell length c length_c	289.050 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	72.360 Å
R factor r_factor	0.2003
R_work r_work	0.1976
R_free r_free	0.2505

Crystal Structure of Coxsackie Virus B3 3D polymerase in complex with GPC-N114 inhibitor

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

3D polymerase

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

4y2a__assembly_1__model_1

4y2a__assembly_1__model_1 | I(q)

4y2a__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of Coxsackie Virus B3 3D polymerase in complex with GPC-N114 inhibitor

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

3D polymerase

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

4y2a__assembly_1__model_1

4y2a__assembly_1__model_1 | I(q)

4y2a__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)