8OS2 | pdb_00008os2

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

PDB DOI: https://doi.org/10.2210/pdb8OS2/pdb

Classification: CELL ADHESION
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2023-04-17 Released: 2024-07-31
Deposition Author(s): Ni, T., Banerji, S., Jackson, D.J., Gilbert, R.J.C.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free:
0.223 (Depositor), 0.223 (DCC)
R-Value Work:
0.183 (Depositor), 0.183 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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: 16.73 kDa
Atom Count: 1,160
Modeled Residue Count: 123
Deposited Residue Count: 146
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lymphatic vessel endothelial hyaluronic acid receptor 1	A	146	Homo sapiens	Mutation(s): 0 Gene Names: LYVE1, CRSBP1, HAR, XLKD1, UNQ230/PRO263
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5Y7 (Homo sapiens) Explore Q9Y5Y7 Go to UniProtKB: Q9Y5Y7
PHAROS: Q9Y5Y7 GTEx: ENSG00000133800
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y5Y7
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A	Go to GlyGen: Q9Y5Y7-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free: 0.223 (Depositor), 0.223 (DCC)
R-Value Work: 0.183 (Depositor), 0.183 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.81	α = 90
b = 70.81	β = 90
c = 75.77	γ = 90

Software Package:

Software Name	Purpose
xia2	data scaling
PHENIX	phasing
PHENIX	refinement
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-31

Deposition Author(s):

Gilbert, R.J.C.

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2024-07-31
Type: Initial release
Version 1.1: 2024-11-13
Changes: Structure summary
Version 1.2: 2025-03-26
Changes: Database references, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.