SMTL ID : 4omm.1

Crystal structure of the intertwined dimer of the c-Src tyrosine kinase SH3 domain mutant N113S

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

PGE.1: 14 residues within 4Å: Chain A: R.32, T.33, T.35, D.36, W.55, Y.68 Chain B: Y.29, R.32, T.33, T.35, D.36, W.55, Y.68 Ligands: PGE.6 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:R.32, B:Y.29, B:R.32, B:R.32, B:T.35, B:D.36 Water bridges: A:T.33, A:T.35, B:T.33 PGE.6: 14 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, D.36, W.55, Y.68 Ligands: PGE.1 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Y.29, A:R.32, A:R.32, A:T.35, B:R.32 Water bridges: A:T.33, B:T.33, B:T.35

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

PEG.2: 3 residues within 4Å: Chain A: Y.27 Chain B: 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.41 PEG.7: 3 residues within 4Å: Chain A: 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 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.41

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: R.65 Chain B: S.31, D.36, L.37, S.38 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.31, B:S.38, B:S.38, B:S.38, B:S.38, A:R.65 Water bridges: B:S.31 GOL.9: 5 residues within 4Å: Chain A: S.31, D.36, L.37, S.38 Chain B: R.65 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.31, A:S.38, A:S.38, A:S.38, A:S.38, B:R.65 Water bridges: A:S.31

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

SO4.5: 5 residues within 4Å: Chain A: T.33, E.34 Chain B: T.33, E.34 Ligands: SO4.10 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.34, B:E.34 SO4.10: 5 residues within 4Å: Chain A: T.33, E.34 Chain B: T.33, E.34 Ligands: SO4.5 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.34, B:E.34, B:E.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Camara-Artigas, A. et al., The role of Gutamine 128 of the SH3 domain of the c-Src tyrosine kinase in 3D domain swapping and amyloid formation. To be Published

Release Date

2015-01-28

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