8QPX

Crystal structure of Geodia cydonium Immunoglobulin-like domain of Receptor Tyrosine Kinase

• PDB DOI: https://doi.org/10.2210/pdb8QPX/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Geodia cydonium
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2023-10-03 Released: 2024-06-26 
• Deposition Author(s): Lopez-Sagaseta, J., Urdiciain, A.
• Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.250 
• R-Value Work: 0.222 
• R-Value Observed: 0.223 

Starting Model: experimental

Literature

Crystal structure of Geodia cydonium Immunoglobulin-like domain of Receptor Tyrosine Kinase

Lopez-Sagaseta, J., Urdiciain, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 26.4 kDa 
• Atom Count: 1,675 
• Modelled Residue Count: 199 
• Deposited Residue Count: 232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor tyrosine kinase (Fragment)	A	232	Geodia cydonium	Mutation(s): 0  Gene Names: TK_2L
UniProt
Find proteins for O18431 (Geodia cydonium) Explore O18431  Go to UniProtKB:  O18431
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help

Entity ID: 2
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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	B	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G82348BZ GlyCosmos:  G82348BZ GlyGen:  G82348BZ

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	I [auth A], J [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.250 
• R-Value Work: 0.222 
• R-Value Observed: 0.223 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.91	α = 90
b = 32.73	β = 90.82
c = 92.05	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-26 
Deposition Author(s): Lopez-Sagaseta, J., Urdiciain, A.

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Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	Margarita Salas
Spanish Ministry of Science, Innovation, and Universities	Spain	RYC-2017-21683

Revision History  

• Version 1.0: 2024-06-26
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Structure summary