5BNP

Crystal structure of human enterovirus D68 in complex with 3'SLN

PDB DOI: https://doi.org/10.2210/pdb5BNP/pdb

Classification: VIRUS
Organism(s): enterovirus D68
Mutation(s): No

Deposited: 2015-05-26 Released: 2015-11-18
Deposition Author(s): Liu, Y., Sheng, J., Meng, G., Xiao, C., Rossmann, M.G.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.246
R-Value Work: 0.244

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 95.7 kDa
Atom Count: 6,677
Modelled Residue Count: 810
Deposited Residue Count: 860
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP1	A	297	enterovirus D68	Mutation(s): 0
UniProt
Find proteins for Q68T42 (Human enterovirus D68) Explore Q68T42 Go to UniProtKB: Q68T42
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q68T42
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP2	B	248	enterovirus D68	Mutation(s): 0
UniProt
Find proteins for Q68T42 (Human enterovirus D68) Explore Q68T42 Go to UniProtKB: Q68T42
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q68T42
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP3	C	247	enterovirus D68	Mutation(s): 0
UniProt
Find proteins for Q68T42 (Human enterovirus D68) Explore Q68T42 Go to UniProtKB: Q68T42
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q68T42
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP4	D	68	enterovirus D68	Mutation(s): 0
UniProt
Find proteins for Q68T42 (Human enterovirus D68) Explore Q68T42 Go to UniProtKB: Q68T42
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q68T42
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	3		N/A	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G00065MO GlyCosmos: G00065MO GlyGen: G00065MO

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900067 Query on PRD_900067	E	3'-sialyl-N-acetyllactosamine	Oligosaccharide / Substrate analog		Interactions Focus chain E Interactions & Density Focus chain E

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.246
R-Value Work: 0.244
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 325.8	α = 90
b = 347.2	β = 90
c = 356.9	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
CNS	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2015-11-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI011219

Revision History (Full details and data files)

Version 1.0: 2015-11-18
Type: Initial release
Version 1.1: 2015-11-25
Changes: Database references
Version 1.2: 2017-09-13
Changes: Author supporting evidence, Other
Version 1.3: 2019-12-11
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary