› 5bmm

X-ray diffraction
2.5Å resolution

Src in complex with DNA-templated macrocyclic inhibitor MC25b

Released:
DOI: 10.2210/pdb5bmm/pdb
PDB entry 5bmm coloured by chain, front view.
PDB entry 5bmm coloured by chain, side view.
PDB entry 5bmm coloured by chain, top view.
Source organisms:
Primary publication:
Structural and Biochemical Basis for Intracellular Kinase Inhibition by Src-specific Peptidic Macrocycles.
Aleem S, Georghiou G, Kleiner RE, Guja K, Craddock BP, Lyczek A, Chan AI, Garcia-Diaz M, Miller WT, Liu DR, Seeliger MA
Cell Chem Biol 23 1103-1112 (2016)
PMID: 27593110

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:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132648 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Proto-oncogene tyrosine-protein kinase Src Chains: A, B
Molecule details ›
Chains: A, B
Length: 286 amino acids
Theoretical weight: 32.73 KDa
Source organism: Gallus gallus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P00523 (Residues: 251-533; Coverage: 53%)
Gene name: SRC
Sequence domains: Protein tyrosine and serine/threonine kinase
Structure domains:
macrocyclic inhibitor MC25b Chains: C, D
Molecule details ›
Chains: C, D
Length: 5 amino acids
Theoretical weight: 741 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
4 modified residues:
Ligand ALC 2 x ALC
Ligand PFF 2 x PFF
Ligand PPN 2 x PPN
Ligand ORN 2 x ORN

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P21
Unit cell:
a: 60.83Å b: 118.61Å c: 42.65Å
α: 90° β: 90.08° γ: 90°
R-values:
R R work R free
0.22 0.218 0.246
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

5 citation in other articles

Second-generation DNA-templated macrocycle libraries for the discovery of bioactive small molecules.
Usanov et al. (2018)
4 more

1 mention without citation

Structural and Biochemical Basis for Intracellular Kinase Inhibition by Src-specific Peptidic Macrocycles.
Aleem et al. (2016)