SMTL ID : 7t1k.1

Crystal structure of a superbinder Fes SH2 domain (sFes1) in complex with a high affinity phosphopeptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

monomer

Ligands

1 x PRO- VAL- PTR- GLU- PRO- VAL: Synthetic phosphotyrosine-containing Ezrin-derived peptide(Non-covalent)

PRO-VAL-PTR-GLU-PRO-VAL.1: 18 residues within 4Å: Chain A: R.16, R.32, G.34, Q.35, S.36, Q.37, V.41, R.51, H.52, F.53, I.54, Q.56, L.64, E.65, T.87, K.89, S.90 Ligands: EDO.6 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:H.52, A:F.53, A:I.54, A:I.54, A:K.89 Hydrogen bonds: A:R.16, A:R.16, A:Q.35, A:S.36, A:S.36, A:Q.37, A:H.52, A:Q.56, A:K.89 Water bridges: A:R.16, A:H.52, A:T.87 Salt bridges: A:R.16, A:R.32, A:R.51 pi-Cation interactions: A:R.16

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

CL.2: 4 residues within 4Å: Chain A: P.15, R.16, A.17, Q.35 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: P.3, L.4, H.5 Ligand excluded by PLIP

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

NA.4: 3 residues within 4Å: Chain A: D.77, L.80, S.81 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.77

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.5: 1 residues within 4Å: Chain A: R.102 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.102, A:R.102

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 3 residues within 4Å: Chain A: Q.37, I.54 Ligands: PRO-VAL-PTR-GLU-PRO-VAL.1 No protein-ligand interaction detected (PLIP) EDO.7: 6 residues within 4Å: Chain A: P.85, T.87, K.88, K.89, S.90, G.91 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martyn, G.D. et al., Engineered SH2 Domains for Targeted Phosphoproteomics. Acs Chem.Biol. (2022)

Release Date

2022-08-24

Peptides

Tyrosine-protein kinase Fes/Fps: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Tyrosine-protein kinase Fes/Fps