2JXA | pdb_00002jxa

Mouse Latrophilin-1 GPCR Gal_lectin domain in complex with Rhamnose

PDB DOI: https://doi.org/10.2210/pdb2JXA/pdb
BMRB: 15553

Classification: CELL ADHESION, SIGNALING PROTEIN
Organism(s): Mus musculus
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2007-11-09 Released: 2008-04-29
Deposition Author(s): Vakonakis, I., Campbell, I.D.

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 50
Conformers Submitted: 25
Selection Criteria: structures with the lowest energy

wwPDB Validation 3D Report Full Report

Validation slider image for 2JXA

This is version 1.3 of the entry. See complete history.

Literature

Solution structure and sugar-binding mechanism of mouse Latrophilin-1 RBL: a novel 7TM receptor-attached lectin-like domain.

Vakonakis, I., Langenhan, T., Promel, S., Russ, A., Campbell, I.D.

To be published.

Macromolecule Content

Total Structure Weight: 12.38 kDa
Atom Count: 859
Modeled Residue Count: 106
Deposited Residue Count: 106
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Latrophilin 1	A	106	Mus musculus	Mutation(s): 0 Gene Names: Lphn1
UniProt
Find proteins for Q80TR1 (Mus musculus) Explore Q80TR1 Go to UniProtKB: Q80TR1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q80TR1
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A	Go to GlyGen: Q80TR1-1
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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain B [auth A]
RAM Query on RAM Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	alpha-L-rhamnopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-HGVZOGFYSA-N		Interactions Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: SOLUTION NMR
Conformers Calculated: 50
Conformers Submitted: 25
Selection Criteria: structures with the lowest energy

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-04-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-04-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.