SMTL ID : 6xvo.1

Crystal structure of the intertwined dimer of the c-Src SH3 domain without ATCUN motif

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 15 residues within 4Å: Chain A: Y.30, R.33, T.34, T.36, D.37, W.56, Y.69 Chain B: Y.30, R.33, T.34, T.36, D.37, W.56, Y.69 Ligands: PGE.4 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:R.33, A:R.33, A:T.36, B:Y.30, B:R.33, B:R.33, B:D.37 Water bridges: A:T.34, B:T.34 PGE.4: 15 residues within 4Å: Chain A: Y.30, R.33, T.34, T.36, D.37, W.56, Y.69 Chain B: Y.30, R.33, T.34, T.36, D.37, W.56, Y.69 Ligands: PGE.1 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:R.33, B:R.33, B:T.36, A:Y.30, A:R.33, A:R.33, A:D.37 Water bridges: B:T.34, A:T.34

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 5 residues within 4Å: Chain A: Y.28 Chain B: T.52, N.73, Y.74 Ligands: PEG.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.73, B:Y.74 PEG.3: 1 residues within 4Å: Ligands: PEG.2 No protein-ligand interaction detected (PLIP) PEG.5: 5 residues within 4Å: Chain A: T.52, N.73, Y.74 Chain B: Y.28 Ligands: PEG.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.73, A:Y.74 PEG.6: 1 residues within 4Å: Ligands: PEG.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Plaza-Garrido, M. et al., The effect of an engineered ATCUN motif on the structure and biophysical properties of the SH3 domain of c-Src tyrosine kinase. J.Biol.Inorg.Chem. (2020)

Release Date

2020-04-22

Peptides

Proto-oncogene tyrosine-protein kinase Src: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Proto-oncogene tyrosine-protein kinase Src

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