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5bno

Crystal structure of human enterovirus D68 in complex with 6'SLN

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Capsid protein VP1

OrganismNot specified

UniProt Q68T42

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Homooligomer Protein 240 其他Polymer 60 N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 60 water × 240 Consistent with protein count
2 Other combination Homooligomer Protein 4 其他Polymer 1 N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 4 Consistent with protein count
3 Other combination Homooligomer Protein 20 其他Polymer 5 N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 5 water × 20 Consistent with protein count
4 Other combination Homooligomer Protein 24 其他Polymer 6 N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 water × 24 Consistent with protein count
5 Other combination Homooligomer Protein 4 其他Polymer 1 N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 4 Consistent with protein count
6 Other combination Homooligomer Protein 60 其他Polymer 15 N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 15 water × 60 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
29hm 29hm 7gnv 7gnv 7gnw 7gnw 7gnx 7gnx 7gny 7gny 7gnz 7gnz

210 assemblies; showing the first 12

Homodimer
8cnx

1 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4wm7 4wm7 4wm7 4wm7 4wm7 4wm7 4wm8 4wm8 4wm8 4wm8 4wm8 4wm8

66 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name Q68T42_9ENTO
Isoform —
PDB entities 1, 2, 3, 4
Chains and sequence ranges Author chain A； PDBConstruct 1–297； UniProt 565–861 Author chain B； PDBConstruct 1–248； UniProt 70–317 Author chain C； PDBConstruct 1–247； UniProt 318–564 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_id5bno
Deposition date deposition_date2015-05-26
Structure title titleCrystal structure of human enterovirus D68 in complex with 6'SLN
Keywords keywordsEnterovirus, Capsid, Beta jelly roll, Virus, Receptor; VIRUS
Experimental Method methodX-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.

5bno__assembly_1__model_1

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

Download this curve (.dat)

5bno__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 1010 1011 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

5bno__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）0.00 Å
Rg (electron density)131.80 Å
Total Rg131.90 Å
Atom count380760
Residues48480
Excluded volume6767100 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5bno__assembly_1__model_1 240-meric （240） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 5bno__assembly_2__model_1 tetrameric （4） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3 1 5bno__assembly_3__model_1 eicosameric （20） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4 1 5bno__assembly_4__model_1 24-meric （24） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5 1 5bno__assembly_5__model_1 tetrameric （4） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6 1 5bno__assembly_6__model_1 60-meric （60） 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)

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5bnoa_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.4 — Positive stranded ssRNA viruses
Family Family familyb.121.4.0 — automated matches
Domain ID domain_idd5bnoc_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.4 — Positive stranded ssRNA viruses
Family Family familyb.121.4.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id5bnoA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
Domain ID domain_id5bnoB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
Domain ID domain_id5bnoC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
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7. Citations (1)