8OX3 | pdb_00008ox3

Structure of the murine LYVE-1 (lymphatic vessel endothelial receptor-1) hyaluronan binding domain bound with octasaccharide hyaluronan.

PDB DOI: https://doi.org/10.2210/pdb8OX3/pdb

Classification: CELL ADHESION
Organism(s): Mus musculus
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2023-04-30 Released: 2025-02-12
Deposition Author(s): Ni, T., Banerji, N., Jackson, D.J., Gilbert, R.J.C.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free:
0.163 (Depositor), 0.162 (DCC)
R-Value Work:
0.151 (Depositor), 0.150 (DCC)
R-Value Observed:
0.151 (Depositor)

Starting Model: experimental
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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

Structure of the murine LYVE-1 (lymphatic vessel endothelial receptor-1) hyaluronan binding domain in an unliganded state

Bano, F., Banerji, S., Ni, T., Green, D.E., DeAngelis, P.L., Paci, E., Lepsik, M., Jackson, D.J., Gilbert, R.J.C.

(2025) Nature Communications

Macromolecule Content

Total Structure Weight: 36.65 kDa
Atom Count: 1,221
Modeled Residue Count: 113
Deposited Residue Count: 318
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lymphatic vessel endothelial hyaluronic acid receptor 1	A	318	Mus musculus	Mutation(s): 0 Gene Names: Lyve1, Crsbp1, Xlkd1
UniProt
Find proteins for Q8BHC0 (Mus musculus) Explore Q8BHC0 Go to UniProtKB: Q8BHC0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8BHC0
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A	Go to GlyGen: Q8BHC0-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid	B [auth C]	6		N/A	Interactions Focus chain B [auth C] Interactions & Density Focus chain B [auth C]
Glycosylation Resources
GlyTouCan: G97733LD GlyCosmos: G97733LD GlyGen: G97733LD

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], H [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]