2N7B

Solution structure of the human Siglec-8 lectin domain in complex with 6'sulfo sialyl Lewisx

PDB DOI: https://doi.org/10.2210/pdb2N7B/pdb
BMRB: 25799

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-09-07 Released: 2016-07-06
Deposition Author(s): Proepster, J.M., Yang, F., Rabbani, S., Ernst, B., Allain, F.H.-T., Schubert, M.

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 500
Conformers Submitted: 20
Selection Criteria: structures with the lowest energy

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 17.64 kDa
Atom Count: 1,240
Modelled Residue Count: 145
Deposited Residue Count: 145
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sialic acid-binding Ig-like lectin 8	A	145	Homo sapiens	Mutation(s): 1 Gene Names: SIGLEC8, SAF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NYZ4 (Homo sapiens) Explore Q9NYZ4 Go to UniProtKB: Q9NYZ4
PHAROS: Q9NYZ4 GTEx: ENSG00000105366
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NYZ4
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-6-O-sulfo-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	B	4		N/A	Interactions Focus chain B
Glycosylation Resources
GlyTouCan: G00672PE GlyCosmos: G00672PE GlyGen: G00672PE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0D8 Query on 0D8 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	3-aminopropan-1-ol C₃ H₉ N O WUGQZFFCHPXWKQ-UHFFFAOYSA-N		Interactions Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: SOLUTION NMR
Conformers Calculated: 500
Conformers Submitted: 20
Selection Criteria: structures with the lowest energy

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-07-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-07-06
Type: Initial release
Version 1.1: 2016-07-27
Changes: Database references
Version 1.2: 2016-08-03
Changes: Database references
Version 1.3: 2016-10-12
Changes: Structure summary
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary

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Deposit Data

Help and Resources

2N7B

Solution structure of the human Siglec-8 lectin domain in complex with 6'sulfo sialyl Lewisx

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)