SAXSdb — 6wdt

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

viral protein 1

Enterovirus D68

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 360	viral protein 2 × 60 （A0A0A7X639） viral protein 4 × 60 （A0A126D252） EV68-228 heavy chain × 60 EV68-228 light chain × 60	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	viral protein 2 × 1 （A0A0A7X639） viral protein 4 × 1 （A0A126D252） EV68-228 heavy chain × 1 EV68-228 light chain × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 30	viral protein 2 × 5 （A0A0A7X639） viral protein 4 × 5 （A0A126D252） EV68-228 heavy chain × 5 EV68-228 light chain × 5	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 36	viral protein 2 × 6 （A0A0A7X639） viral protein 4 × 6 （A0A126D252） EV68-228 heavy chain × 6 EV68-228 light chain × 6	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 6	viral protein 2 × 1 （A0A0A7X639） viral protein 4 × 1 （A0A126D252） EV68-228 heavy chain × 1 EV68-228 light chain × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A097BW12_9ENTO
Isoform	—
PDB entities	1, 3
Chains and sequence ranges	Author chain A； PDBConstruct 1–297； UniProt 565–861 Author chain C； PDBConstruct 1–247； UniProt 318–564

viral protein 2

Enterovirus D68

UniProt A0A0A7X639

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 360	viral protein 1 × 60 （A0A097BW12） viral protein 3 × 60 （A0A097BW12） viral protein 4 × 60 （A0A126D252） EV68-228 heavy chain × 60 EV68-228 light chain × 60	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	viral protein 1 × 1 （A0A097BW12） viral protein 3 × 1 （A0A097BW12） viral protein 4 × 1 （A0A126D252） EV68-228 heavy chain × 1 EV68-228 light chain × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 30	viral protein 1 × 5 （A0A097BW12） viral protein 3 × 5 （A0A097BW12） viral protein 4 × 5 （A0A126D252） EV68-228 heavy chain × 5 EV68-228 light chain × 5	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 36	viral protein 1 × 6 （A0A097BW12） viral protein 3 × 6 （A0A097BW12） viral protein 4 × 6 （A0A126D252） EV68-228 heavy chain × 6 EV68-228 light chain × 6	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 6	viral protein 1 × 1 （A0A097BW12） viral protein 3 × 1 （A0A097BW12） viral protein 4 × 1 （A0A126D252） EV68-228 heavy chain × 1 EV68-228 light chain × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0A7X639_9ENTO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–248； UniProt 70–317

viral protein 4

Enterovirus D68

UniProt A0A126D252

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 360	viral protein 1 × 60 （A0A097BW12） viral protein 2 × 60 （A0A0A7X639） viral protein 3 × 60 （A0A097BW12） EV68-228 heavy chain × 60 EV68-228 light chain × 60	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	viral protein 1 × 1 （A0A097BW12） viral protein 2 × 1 （A0A0A7X639） viral protein 3 × 1 （A0A097BW12） EV68-228 heavy chain × 1 EV68-228 light chain × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 30	viral protein 1 × 5 （A0A097BW12） viral protein 2 × 5 （A0A0A7X639） viral protein 3 × 5 （A0A097BW12） EV68-228 heavy chain × 5 EV68-228 light chain × 5	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 36	viral protein 1 × 6 （A0A097BW12） viral protein 2 × 6 （A0A0A7X639） viral protein 3 × 6 （A0A097BW12） EV68-228 heavy chain × 6 EV68-228 light chain × 6	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 6	viral protein 1 × 1 （A0A097BW12） viral protein 2 × 1 （A0A0A7X639） viral protein 3 × 1 （A0A097BW12） EV68-228 heavy chain × 1 EV68-228 light chain × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A126D252_9ENTO
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–68； UniProt 2–69

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	6wdt
Deposition date deposition_date	2020-04-01
Structure title title	Enterovirus D68 in complex with human monoclonal antibody EV68-228
Keywords keywords	;virus, enterovirus, antibody, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRUS-IMMUNE SYSTEM complex ;; VIRUS/IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

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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.

6wdt__assembly_1__model_1

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

Download this curve (.dat)

6wdt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6wdt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	0.00 Å
Rg (electron density)	140.80 Å
Total Rg	140.90 Å
Atom count	478740
Residues	61680
Excluded volume	8496000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6wdt__assembly_1__model_1`	360-meric （360）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6wdt__assembly_2__model_1`	hexameric （6）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`6wdt__assembly_3__model_1`	30-meric （30）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`6wdt__assembly_4__model_1`	36-meric （36）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`6wdt__assembly_5__model_1`	hexameric （6）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.

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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	viral protein 1
Molecular weight formula_weight	32920.3 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	7979

IESIIKTATDTVKSEINAELGVVPSLNAVETGATSNTEPEEAIQTRTVINQHGVSETLVENFLSRAALVSKRSFEYKDHTSSTARADKNFFKWTINTRSFVQLRRKLELFTYLRFDAEITILTTVAVNGSGNNTYVGLPDLTLQAMFVPTGALTPEKQDSFHWQSGSNASVFFKISDPPARITIPFMCINSAYSVFYDGFAGFEKNGLYGINPADTIGNLCVRIVNEHQPVGFTVTVRVYMKPKHIKAWAPRPPRTLPYMSIANANYKGKERAPNALSAIIGNRDSVKTMPHNIVNT

Source Source

Source organism organism	Enterovirus D68
NCBI taxonomy ID ncbi_taxonomy_id	42789
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	viral protein 2
Molecular weight formula_weight	27567.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SPSAEACGYSDRVLQLKLGNSAIVTQEAANYCCAYGEWPNYLPDHEAVAIDKPTQPETATDRFYTLKSVKWETGSTGWWWKLPDALNNIGMFGQNVQHHYLYRSGFLIHVQCNATKFHQGALLVVAIPEHQRGAHNTNTSPGFDDIMKGEEGGTFNHPYVLDDGTSLACATIFPHQWINLRTNNSATIVLPWMNAAPMDFPLRHNQWTLAIIPVVPLGTRTTSSMVPITVSIAPMCCEFNGLRHAITQ

Source Source

Source organism organism	Enterovirus D68
NCBI taxonomy ID ncbi_taxonomy_id	42789
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	viral protein 3
Molecular weight formula_weight	27112.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GVPTYLLPGSGQFLTTDDHSSAPALPCFNPTPEMHIPGQVRNMLEVVQVESMMEINNTESAVGMERLKVDISALTDVDQLLFNIPLDIQLDGPLRNTLVGNISRYYTHWSGSLEMTFMFCGSFMAAGKLILCYTPPGGSCPTTRETAMLGTHIVWDFGLQSSVTLIIPWISGSHYRMFNNDAKSTNANVGYVTCFMQTNLIVPSESSDTCSLIGFIAAKDDFSLRLMRDSPDIGQLDHLHAAEAAYQ

Source Source

Source organism organism	Enterovirus D68
NCBI taxonomy ID ncbi_taxonomy_id	42789
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	viral protein 4
Molecular weight formula_weight	7337.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GAQVTRQQTGTHENANIATNGSHITYNQINFYKDSYAASASKQDFSQDPSKFTEPVVEGLKAGAPVLK

Source Source

Source organism organism	Enterovirus D68
NCBI taxonomy ID ncbi_taxonomy_id	42789
Host organism host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	EV68-228 heavy chain
Molecular weight formula_weight	14037.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QVQLQESGPGLVKPSETLSLTCTVSGYLISNGYYWGWIRQSPGKGLEWIGSIYYTRDTYYNWSLKSRITISVDTSKKQFSLKLYSVTAADTAVYYCVRHEGSCNDGSCYGSFVDNWGQGTLVTVSS

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Cricetulus griseus

Entity 6 Entity 6 polymer

Description description	EV68-228 light chain
Molecular weight formula_weight	11354.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIQMTQSPSSVSASVGDRVTLTCRASQDISSWLAWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTHFTLTISSLQPEDFATYFCQQADSFITFGGGTKVEIK

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Cricetulus griseus

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d6wdta_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.0 — automated matches

Domain ID domain_id	d6wdtc_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.0 — automated matches

Domain ID domain_id	d6wdth1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6wdth2
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	d6wdtl_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

CATH v4.4 (3 domains)

Domain ID domain_id	6wdtA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	6wdtB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	6wdtC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	3.10 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	20194

Enterovirus D68 in complex with human monoclonal antibody EV68-228

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

viral protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

viral 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

viral protein 4

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

6wdt__assembly_1__model_1

6wdt__assembly_1__model_1 | I(q)

6wdt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (5 domains)

CATH v4.4 (3 domains)

7. Citations (1)