SMTL ID : 5jvx.1

X-ray structure of the adduct formed in the reaction between thaumatin and a gold carbene compound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

2 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.1: 5 residues within 4Å: Chain A: G.96, K.97, P.194, G.195, S.196 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.96, A:G.195, A:G.195, A:G.195, A:G.195 Water bridges: A:S.196 Salt bridges: A:K.97 TLA.2: 4 residues within 4Å: Chain A: R.29, E.35, S.36, W.37 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.29, A:R.29, A:S.36, A:S.36, A:S.36, A:S.36, A:S.36 Salt bridges: A:R.29

6 x 6O0: (1-butyl-3-methyl-1,3-dihydro-2H-imidazol-2-ylidene)(chloro)gold(Covalent)(Non-covalent)

6O0.3: 6 residues within 4Å: Chain A: A.1, T.2, N.40, V.41, E.42, P.43 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.40 6O0.4: 10 residues within 4Å: Chain A: K.49, W.51, F.80, G.81, R.82, P.83, T.85, L.87, K.106 Ligands: 6O0.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.51, A:W.51, A:F.80, A:T.85, A:L.87 pi-Cation interactions: A:K.106 6O0.5: 7 residues within 4Å: Chain A: F.80, G.81, R.82, P.83, K.106, T.150 Ligands: 6O0.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.82, A:T.150 6O0.6: 2 residues within 4Å: Chain A: K.97, T.192 No protein-ligand interaction detected (PLIP) 6O0.7: 4 residues within 4Å: Chain A: R.8, R.125, T.202, P.205 No protein-ligand interaction detected (PLIP) 6O0.8: 2 residues within 4Å: Chain A: F.172, R.175 No protein-ligand interaction detected (PLIP)

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

CL.9: 3 residues within 4Å: Chain A: V.131, G.143, G.144 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferraro, G. et al., First Crystal Structure for a Gold Carbene-Protein Adduct. Bioconjug.Chem. (2016)

Release Date

2016-07-13

Peptides

Thaumatin-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Thaumatin-1

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