SMTL ID : 3ov1.2 (1 other biounit)

Crystal Structure of the Grb2 SH2 Domain in Complex with a pYXN-Derived Tripeptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x ACT- PTR- 1AC- ASN- NH2: PYAC3CN(Non-covalent)

ACT-PTR-1AC-ASN-NH2.1: 11 residues within 4Å: Chain A: R.15, R.34, S.36, S.38, S.44, H.55, F.56, K.57, L.59, L.68, W.69 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:H.55, A:F.56, A:K.57, A:W.69 Hydrogen bonds: A:R.15, A:R.15, A:S.36, A:S.38, A:S.38, A:S.44, A:H.55, A:K.57, A:L.68 Water bridges: A:R.34, A:E.37, A:S.38, A:K.57, A:K.57, A:K.57, A:K.57 Salt bridges: A:R.15, A:R.34 ACT-PTR-1AC-ASN-NH2.6: 11 residues within 4Å: Chain B: R.15, R.34, S.36, S.38, S.44, H.55, F.56, K.57, L.59, L.68, W.69 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:H.55, B:F.56, B:K.57, B:W.69 Hydrogen bonds: B:R.15, B:R.15, B:S.36, B:S.38, B:S.38, B:S.44, B:H.55, B:K.57, B:L.68 Water bridges: B:R.34, B:E.37, B:S.38, B:K.57, B:K.57, B:K.57, B:K.57 Salt bridges: B:R.15, B:R.34

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: D.42, L.59, R.60 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.42, A:R.60, A:R.60 GOL.3: 6 residues within 4Å: Chain A: W.69, H.83, T.86, S.87, S.89, R.90 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.89, A:R.90 Water bridges: A:W.69 GOL.7: 3 residues within 4Å: Chain B: D.42, L.59, R.60 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.42, B:R.60, B:R.60 GOL.8: 6 residues within 4Å: Chain B: W.69, H.83, T.86, S.87, S.89, R.90 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.89, B:R.90 Water bridges: B:W.69

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

FMT.4: 5 residues within 4Å: Chain A: K.24, Q.25, R.26, H.27, E.100 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.24, A:R.26 Water bridges: A:H.27, A:H.27 FMT.9: 5 residues within 4Å: Chain B: K.24, Q.25, R.26, H.27, E.100 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.24, B:R.26, B:H.27 Water bridges: B:H.27, B:H.27

2 x NA: SODIUM ION(Non-functional Binders)

NA.5: 3 residues within 4Å: Chain A: D.42, F.43, V.58 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.43, A:F.43 Water bridges: A:R.60 NA.10: 3 residues within 4Å: Chain B: D.42, F.43, V.58 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.43, B:F.43 Water bridges: B:R.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Myslinski, J.M. et al., Protein-ligand interactions: thermodynamic effects associated with increasing nonpolar surface area. J.Am.Chem.Soc. (2011)

Release Date

2011-11-02

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

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