SMTL ID : 4oml.1

Crystal structure of the intertwined dimer of the c-Src tyrosine kinase SH3 domain mutant Q128R

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

PGE.1: 13 residues within 4Å: Chain A: Y.29, R.32, T.33, T.35, D.36, W.55, Y.68 Chain B: R.32, T.33, T.35, W.55, Y.68 Ligands: PGE.5 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.29, A:R.32, A:R.32, A:D.36, B:R.32, B:R.32 PGE.5: 13 residues within 4Å: Chain A: R.32, T.33, T.35, W.55, Y.68 Chain B: Y.29, R.32, T.33, T.35, D.36, W.55, Y.68 Ligands: PGE.1 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.29, B:R.32, B:R.32, B:D.36, A:R.32, A:R.32

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

PEG.2: 4 residues within 4Å: Chain A: Y.27 Chain B: T.51, N.72, Y.73 No protein-ligand interaction detected (PLIP) PEG.3: 6 residues within 4Å: Chain A: V.24, A.25, L.26, K.41, G.42 Ligands: PEG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.41 PEG.4: 7 residues within 4Å: Chain A: K.40, K.41, G.42, E.43 Chain B: T.62, T.63 Ligands: PEG.3 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.43 Water bridges: A:K.40, A:E.43, A:R.44, B:T.62 PEG.6: 4 residues within 4Å: Chain A: T.51, N.72, Y.73 Chain B: Y.27 No protein-ligand interaction detected (PLIP) PEG.7: 6 residues within 4Å: Chain B: V.24, A.25, L.26, K.41, G.42 Ligands: PEG.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.41 PEG.8: 7 residues within 4Å: Chain A: T.62, T.63 Chain B: K.40, K.41, G.42, E.43 Ligands: PEG.7 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:K.40, B:E.43, B:R.44, A:T.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bacarizo, J. et al., Electrostatic Effects in the Folding of the SH3 Domain of the c-Src Tyrosine Kinase: pH-Dependence in 3D-Domain Swapping and Amyloid Formation. Plos One (2014)

Release Date

2014-12-10

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