SMTL ID : 4omn.1

Crystal structure of the intertwined dimer of the c-Src tyrosine kinase SH3 domain mutant Q128E

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

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

PGE.1: 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.6 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.29, B:Y.29, B:R.32, B:R.32, A:R.32 Water bridges: B:T.35, A:T.35 PGE.6: 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.1 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:R.32, A:Y.29, A:Y.29, A:R.32, A:R.32 Water bridges: B:T.35, A:T.35

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

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 5 residues within 4Å: Chain A: T.33, E.34 Chain B: T.33, E.34 Ligands: SO4.9 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.34, B:E.34 SO4.9: 5 residues within 4Å: Chain A: T.33, E.34 Chain B: T.33, E.34 Ligands: SO4.4 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.34, B:E.34 Water bridges: B:E.34, B:E.34

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: D.28, Y.29, E.30, S.38, F.39, K.40 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.29, A:F.39 Water bridges: A:S.38, A:K.40 GOL.10: 6 residues within 4Å: Chain B: D.28, Y.29, E.30, S.38, F.39, K.40 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.29, B:F.39 Water bridges: B:S.38, B:K.40

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