13yz

PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3Dpol in complex with Z285233820

Method: X-RAY DIFFRACTION

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

3Dpol RNA Dependent RNA Polymerase

enterovirus D68

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ISOPROPYL ALCOHOL × 15 DI(HYDROXYETHYL)ETHER × 1 GLYCEROL × 1 (5M)-5-(2-methoxyphenyl)-1,3,4-oxadiazol-2-amine × 2 MAGNESIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	F1T146_HED68
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–457； UniProt 1732–2188

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	13yz
Deposition date deposition_date	2026-03-06
Last revision last_revision	2026-03-18
Structure title title	PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3Dpol in complex with Z285233820
Keywords keywords	SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, RNA-dependent RNA polymerase, TRANSFERASE; 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.

13yz__assembly_1__model_1

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

Download this curve (.dat)

13yz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

13yz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.15 Å
Rg (electron density)	23.02 Å
Total Rg	24.00 Å
Atom count	3741
Residues	457
Excluded volume	67317 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`13yz__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 (7)

Entity 1 Entity 1 polymer

Description description	3Dpol RNA Dependent RNA Polymerase
Molecular weight formula_weight	52958.3 kDa
EC 编号 ec_number	3.4.22.29,3.6.1.15,3.4.22.28,2.7.7.48
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	4063

GEIVSNEKSGVCINAPAKTKLQPSVFHQVFEGSKEPAVLNSKDPRLKTDFEEAIFSKYTGNKIMLMDEYMEEAVDHYVGCLEPLDISVDPIPLESAMYGMDGLEALDLTTSAGFPYLLQGKKKRDIFNRHTRDTTEMTKMLEKYGVDLPFVTFVKDELRSKEKVEKGKSRLIEASSLNDSVAMRVAFGNLYATFHSNPGTATGSAVGCDPDIFWSKIPILLDGEIFAFDYTGYDASLSPVWFACLKKVLIKLGYTHQTSFIDYLCHSVHLYKDRKYIVNGGMPSGSSGTSIFNTMINNIIIRTLLIRVYKGIDLDQFKMIAYGDDVIASYPHKIDPALLAEAGKHYGLVMTPADKGTSFVDTNWENVTFLKRYFRADDQYPFLIHPVMPMKEIHESIRWTKDPRNTQDHVRSLCYLAWHNGEEAYNEFCRKIRSVPVGRALTLPAYSSLRRKWLDSFGSSGHHHHHH

Source Source

Source organism organism	enterovirus D68
NCBI taxonomy ID ncbi_taxonomy_id	42789
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ISOPROPYL ALCOHOL
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 3 Entity 3 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	(5M)-5-(2-methoxyphenyl)-1,3,4-oxadiazol-2-amine
Molecular weight formula_weight	191.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	322

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Unit-cell length a length_a	55.281 Å
Unit-cell length b length_b	83.730 Å
Unit-cell length c length_c	58.922 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.42 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	55.900 Å
R factor r_factor	0.1864
R_work r_work	0.1849
R_free r_free	0.2155

PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3Dpol in complex with Z285233820

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

3Dpol RNA Dependent RNA 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

13yz__assembly_1__model_1

13yz__assembly_1__model_1 | I(q)

13yz__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 (7)

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 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3Dpol in complex with Z285233820

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

3Dpol RNA Dependent RNA 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

13yz__assembly_1__model_1

13yz__assembly_1__model_1 | I(q)

13yz__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 (7)

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 non-polymer

Entity 7 Entity 7 water

7. Citations (1)