1ETE | pdb_00001ete

CRYSTAL STRUCTURE OF THE FLT3 LIGAND

PDB DOI: https://doi.org/10.2210/pdb1ETE/pdb

Classification: CYTOKINE
Organism(s): Homo sapiens
Expression System: Bacteria
Mutation(s): No

Deposited: 2000-04-12 Released: 2000-06-14
Deposition Author(s): Savvides, S.N., Boone, T., Karplus, P.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.287 (Depositor)
R-Value Work:
0.239 (Depositor), 0.248 (DCC)

wwPDB Validation 3D Report Full Report

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

Literature

Flt3 ligand structure and unexpected commonalities of helical bundles and cystine knots.

Savvides, S.N., Boone, T., Andrew Karplus, P.

(2000) Nat Struct Biol 7: 486-491

PubMed: 10881197 Search on PubMed
DOI: https://doi.org/10.1038/75896
Primary Citation Related Structures:
1ETE

PubMed Abstract:
Human Flt3 ligand (Flt3L) stimulates early hematopoiesis by activating a type III tyrosine kinase receptor on primitive bone marrow stem cells. The crystal structure of soluble Flt3L reveals that it is a homodimer of two short chain alpha-helical bundles. Comparisons of structure-function relationships of Flt3L with the homologous hematopoietic cytokines macrophage colony stimulating factor (MCSF) and stem cell factor (SCF) suggest that they have a common receptor binding mode that is distinct from the paradigm derived from the complex of growth hormone with its receptor. Furthermore, we identify recognition features common to all helical and cystine-knot protein ligands that activate type III tyrosine kinase receptors, and the closely related type V tyrosine kinase receptors.

Organizational Affiliation

Program in Biophysics, Cornell University, Ithaca, NY 14853, USA.

Macromolecule Content

Total Structure Weight: 62.37 kDa
Atom Count: 4,494
Modeled Residue Count: 529
Deposited Residue Count: 536
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FLT3 LIGAND	A, B, C, D	134	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P49771 (Homo sapiens) Explore P49771 Go to UniProtKB: P49771
GTEx: ENSG00000090554
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49771
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain M [auth D] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain M [auth D] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth B] I [auth B] E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth C], L [auth C], M [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.287 (Depositor)
R-Value Work: 0.239 (Depositor), 0.248 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.08	α = 90
b = 159.41	β = 90
c = 26.25	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASES	phasing
X-PLOR	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2000-06-14

Deposition Author(s):

Savvides, S.N.

Boone, T.

Karplus, P.A.

Revision History (Full details and data files)

Version 1.0: 2000-06-14
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary