7ZV9

Crystal structure of FLT3 in complex with a monomeric FLT3 Ligand variant

• PDB DOI: https://doi.org/10.2210/pdb7ZV9/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Homo sapiens
• Mutation(s): Yes 


• Deposited: 2022-05-14 Released: 2023-05-31 
• Deposition Author(s): Pannecoucke, E., Savvides, S.N.
• Funding Organization(s): Research Foundation - Flanders (FWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.51 Å
• R-Value Free: 0.291 
• R-Value Work: 0.278 
• R-Value Observed: 0.278 

Literature

Crystal structure of FLT3 in complex with a monomeric FLT3 Ligand variant

Pannecoucke, E., Savvides, S.N.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 5 assigned by authors.

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 6 assigned by authors.

Biological Assembly 7  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 7 assigned by authors.

Biological Assembly 8  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 8 assigned by authors.

Macromolecule Content

• Total Structure Weight: 668.01 kDa 
• Atom Count: 26,691 
• Modelled Residue Count: 4,466 
• Deposited Residue Count: 5,896 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fms-related tyrosine kinase 3 ligand	A, C, E, G, I, K, M, O	155	Homo sapiens	Mutation(s): 1  Gene Names: FLT3LG
UniProt & NIH Common Fund Data Resources
Find proteins for P49771 (Homo sapiens) Explore P49771  Go to UniProtKB:  P49771
GTEx:  ENSG00000090554

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-type tyrosine-protein kinase FLT3	B, D, F, H, J, L, N, P	582	Homo sapiens	Mutation(s): 0  Gene Names: FLT3, CD135, FLK2, STK1 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P36888 (Homo sapiens) Explore P36888  Go to UniProtKB:  P36888
PHAROS:  P36888 GTEx:  ENSG00000122025

Oligosaccharides

Help

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	Q, R, S, T, U, V	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	W [auth B], X [auth B], Y [auth H], Z [auth P]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.51 Å
• R-Value Free: 0.291 
• R-Value Work: 0.278 
• R-Value Observed: 0.278 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.208	α = 90.02
b = 139.215	β = 90.03
c = 143.689	γ = 89.99

Software Package:

Software Name	Purpose
BUSTER	refinement
PHENIX	refinement
XDS	data scaling
PHASER	phasing
Coot	model building
PDB-REDO	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-31 
Deposition Author(s): Pannecoucke, E., Savvides, S.N.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	--

Revision History  

• Version 1.0: 2023-05-31
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description