8SUF

The complex of TOL-1 ectodomain bound to LAT-1 Lectin domain

PDB DOI: https://doi.org/10.2210/pdb8SUF/pdb

Classification: CELL ADHESION
Organism(s): Caenorhabditis elegans
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2023-05-12 Released: 2024-05-15
Deposition Author(s): Carmona Rosas, G., Li, J., Arac, D., Ozkan, E.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.00 Å
R-Value Free: 0.338
R-Value Work: 0.288
R-Value Observed: 0.291

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural basis and functional roles for Toll-like receptor binding to Latrophilin adhesion-GPCR in embryo development

Carmona Rosas, G., Li, J., Smith, J.S., Cheng, S., Baltrusaitis, E., Nawrocka, W.I., Zhao, M., Kratsios, P., Arac, D., Ozkan, E.

To be published.

Macromolecule Content

Total Structure Weight: 507.34 kDa
Atom Count: 32,993
Modelled Residue Count: 4,180
Deposited Residue Count: 4,484
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TIR domain-containing protein	A, B, C, D	1,007	Caenorhabditis elegans	Mutation(s): 0 Gene Names: tol-1, C07F11.1, CELE_C07F11.1
UniProt
Find proteins for Q9N5Z3 (Caenorhabditis elegans) Explore Q9N5Z3 Go to UniProtKB: Q9N5Z3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9N5Z3
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Latrophilin-like protein 1	E, F, G, H	114	Caenorhabditis elegans	Mutation(s): 0 Gene Names: lat-1, B0457.1
UniProt
Find proteins for G5EDW2 (Caenorhabditis elegans) Explore G5EDW2 Go to UniProtKB: G5EDW2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G5EDW2
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I, M	4		N-Glycosylation	Interactions Focus chain I Focus chain M Interactions & Density Focus chain I Focus chain M
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J, K, N, O, R	2		N-Glycosylation	Interactions Focus chain J Focus chain K Focus chain N Focus chain O Focus chain R Interactions & Density Focus chain J Focus chain K Focus chain N Focus chain O Focus chain R
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L	4		N-Glycosylation	Interactions Focus chain L Interactions & Density Focus chain L
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	P	5		N-Glycosylation	Interactions Focus chain P Interactions & Density Focus chain P
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	Q	3		N-Glycosylation	Interactions Focus chain Q Interactions & Density Focus chain Q
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	AA [auth D] BA [auth D] S [auth A] T [auth A] U [auth A] AA [auth D], BA [auth D], S [auth A], T [auth A], U [auth A], V [auth B], W [auth B], X [auth B], Y [auth C], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth C] Focus chain Z [auth C]