› 6fnk

X-ray diffraction
1.05Å resolution

Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase with a pyrazolo[3,4-d]pyrimidine fragment of NVP-BHG712

Released:
DOI: 10.2210/pdb6fnk/pdb
PDB entry 6fnk coloured by chain, front view.
PDB entry 6fnk coloured by chain, side view.
PDB entry 6fnk coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family.
Tröster A, Heinzlmeir S, Berger BT, Gande SL, Saxena K, Sreeramulu S, Linhard V, Nasiri AH, Bolte M, Müller S, Kuster B, Médard G, Kudlinzki D, Schwalbe H
ChemMedChem 13 1629-1633 (2018)
PMID: 29928781

Function and Biology Details

Reaction catalysed: 
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-157090 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ephrin type-B receptor 4 Chain: A
Molecule details ›
Chain: A
Length: 297 amino acids
Theoretical weight: 33.49 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P54760 (Residues: 598-892; Coverage: 30%)
Gene names: EPHB4, HTK, MYK1, TYRO11
Sequence domains: Protein tyrosine and serine/threonine kinase
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand DXK 1 x DXK
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID30B
Spacegroup: P21
Unit cell:
a: 45.522Å b: 53.577Å c: 61.345Å
α: 90° β: 110.55° γ: 90°
R-values:
R R work R free
0.196 0.198 0.22
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

EphrinB2-EphB4 Signaling in Neurooncological Disease.
Piffko et al. (2022)
1 more