7LIR

Structure of the invertebrate ALK GRD

• PDB DOI: https://doi.org/10.2210/pdb7LIR/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Caenorhabditis elegans
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2021-01-27 Released: 2021-11-24 
• Deposition Author(s): Stayrook, S., Li, T., Klein, D.E.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.270 
• R-Value Work: 0.223 
• R-Value Observed: 0.226 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 81.46 kDa 
• Atom Count: 5,660 
• Modelled Residue Count: 683 
• Deposited Residue Count: 700 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALK tyrosine kinase receptor homolog scd-2	A, B	350	Caenorhabditis elegans	Mutation(s): 0  Gene Names: scd-2, T10H9.2 EC: 2.7.10.1
UniProt
Find proteins for O76411 (Caenorhabditis elegans) Explore O76411  Go to UniProtKB:  O76411

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	6	N/A	N-Glycosylation
Glycosylation Resources
GlyTouCan:  G51784HB GlyCosmos:  G51784HB GlyGen:  G51784HB

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, F, I	2	N/A	N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2	N/A	N-Glycosylation
Glycosylation Resources
GlyTouCan:  G35446HX GlyCosmos:  G35446HX GlyGen:  G35446HX

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G	5	N/A	N-Glycosylation
Glycosylation Resources
GlyTouCan:  G93904UY GlyCosmos:  G93904UY

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	3	N/A	N-Glycosylation
Glycosylation Resources
GlyTouCan:  G62182OO GlyCosmos:  G62182OO GlyGen:  G62182OO

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	L [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	J [auth A], K [auth A], M [auth B], N [auth B], O [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.270 
• R-Value Work: 0.223 
• R-Value Observed: 0.226 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 224.339	α = 90
b = 224.339	β = 90
c = 114.525	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
SHELX	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-11-24 
Deposition Author(s): Stayrook, S., Li, T., Klein, D.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	K22 CA215821
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01 CA248532

Revision History  

• Version 1.0: 2021-11-24
  Type: Initial release
  
• Version 1.1: 2021-12-08
  Changes: Database references
• Version 1.2: 2021-12-15
  Changes: Database references