SMTL ID : 3c7i.1

X-RAY crystal structure of the complex between the grb2-sh2 domain and a flexible ligand, FPTVN.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x TVN: N-{(2R)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-valyl-L-aspartamide(Non-covalent)

TVN.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 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Q.54, A:H.55, A:F.56, A:K.57, A:W.69 Hydrogen bonds: A:R.15, A:R.15, A:S.38, A:S.38, A:S.44, A:H.55, A:K.57, A:K.57 Water bridges: A:R.34, A:R.34, A:H.55, A:K.57, A:K.57, A:K.57, A:K.57 Salt bridges: A:R.15, A:R.34 TVN.3: 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 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:Q.54, B:H.55, B:F.56, B:K.57, B:W.69 Hydrogen bonds: B:R.15, B:R.15, B:S.38, B:S.38, B:S.44, B:H.55, B:K.57, B:K.57 Water bridges: B:R.34, B:R.34, B:H.55, B:K.57, B:K.57, B:K.57, B:K.57 Salt bridges: B:R.15, B:R.34

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 4 residues within 4Å: Chain A: Q.25, R.26, H.27, E.100 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.26, A:E.100, A:E.100 Water bridges: A:H.27, A:H.27 FMT.4: 4 residues within 4Å: Chain B: Q.25, R.26, H.27, E.100 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.26, B:H.27, B:E.100 Water bridges: B:H.27, B:H.27

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Benfield, A.P. et al., Ligand Preorganization May be Accompanied by Entropic Penalties in Protein-Ligand Interactions. Angew.Chem.Int.Ed.Engl. (2006)

Release Date

2008-08-12

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

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