7QDP | pdb_00007qdp

Crystal structure of FLT3 T343I in complex with the canonical ligand FL

• PDB DOI: https://doi.org/10.2210/pdb7QDP/pdb

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


• Deposited: 2021-11-27 Released: 2022-12-14 
• 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: 3.69 Å
• R-Value Free: 
  0.277 (Depositor), 0.340 (DCC) 
• R-Value Work: 
  0.257 (Depositor), 0.319 (DCC) 
• R-Value Observed: 
  0.258 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of FLT3 T343I in complex with the canonical ligand FL

Pannecoucke, E., Savvides, S.N.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A4B3C1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 8-mer - A4B4 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 334.22 kDa 
• Atom Count: 13,508 
• Modeled Residue Count: 1,960 
• Deposited Residue Count: 2,948 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fms-related tyrosine kinase 3 ligand	A, B, C, D	155	Homo sapiens	Mutation(s): 0  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	E, F, G, H	582	Homo sapiens	Mutation(s): 2  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
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P36888-1

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J	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	K [auth E], L [auth F], M [auth F], N [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.69 Å
• R-Value Free:  0.277 (Depositor), 0.340 (DCC) 
• R-Value Work:  0.257 (Depositor), 0.319 (DCC) 
• R-Value Observed: 0.258 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.428	α = 105.37
b = 113.377	β = 109.47
c = 123.225	γ = 108.22

Software Package:

Software Name	Purpose
BUSTER	refinement
MxCuBE	data collection
XDS	data reduction
XDS	data scaling
Coot	model building
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-12-14 
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: 2022-12-14
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary