SMTL ID : 3kfj.2 (1 other biounit)

Crystal Structure of the Grb2 SH2 Domain in Complex with a Flexible Ac-pY-E-N-NH2 Tripeptide Mimic

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-dimer

Ligands

2 x YEN: N-{(2S)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-alpha-glutamyl-L-aspartamide(Non-covalent)

YEN.1: 12 residues within 4Å: Chain A: R.15, R.34, S.36, S.38, S.44, Q.54, H.55, F.56, K.57, L.59, L.68, W.69 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Q.54, A:F.56, A:K.57, A:W.69 Hydrogen bonds: A:R.15, A:R.15, A:S.38, A:S.44, A:S.44, A:H.55, A:K.57, A:L.68 Water bridges: A:E.37, A:H.55, A:K.57, A:K.57 Salt bridges: A:R.15, A:R.34 YEN.5: 12 residues within 4Å: Chain B: R.15, R.34, S.36, S.38, S.44, Q.54, H.55, F.56, K.57, L.59, L.68, W.69 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Q.54, B:F.56, B:K.57, B:W.69 Hydrogen bonds: B:R.15, B:R.15, B:S.38, B:S.44, B:S.44, B:H.55, B:K.57, B:L.68 Water bridges: B:E.37, B:H.55, B:K.57, B:K.57 Salt bridges: B:R.15, B:R.34

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 3 residues within 4Å: Chain A: Q.25, R.26, E.100 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: L.59, R.60 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain B: Q.25, R.26, E.100 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain B: L.59, R.60 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: T.86, S.87, Q.93, F.95 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: T.86, S.87, Q.93, F.95 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

DeLorbe, J.E. et al., Thermodynamic and structural effects of conformational constraints in protein-ligand interactions. Entropic paradoxy associated with ligand preorganization. J.Am.Chem.Soc. (2009)

Release Date

2010-03-02

Peptides

Growth factor receptor-bound protein 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Growth factor receptor-bound protein 2

Related Entries With Identical Sequence