SMTL ID : 3o98.1

Glutathionylspermidine synthetase/amidase C59A complex with ADP and Gsp

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

1 x TS5: GLUTATHIONYLSPERMIDINE(Non-covalent)

TS5.1: 15 residues within 4Å: Chain A: Y.52, G.54, Q.58, A.59, V.60, R.64, D.77, V.78, G.79, M.80, A.81, T.129, G.130, H.131, N.149 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.60, A:N.149 Hydrogen bonds: A:Q.58, A:A.59, A:D.77, A:V.78, A:G.79, A:A.81, A:G.130, A:N.149 Water bridges: A:Q.58 Salt bridges: A:R.64

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 25 residues within 4Å: Chain A: D.318, Y.329, E.330, K.498, A.531, K.533, G.537, R.538, C.539, G.540, S.541, I.543, L.545, Q.568, Q.569, L.570, W.571, C.572, L.573, Q.582, L.603, V.604, I.605 Ligands: MG.3, MG.4 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:D.318, A:D.318, A:K.533, A:C.539, A:G.540, A:S.541, A:Q.568, A:Q.569, A:W.571, A:Q.582, A:I.605 Water bridges: A:R.316, A:N.332, A:N.332, A:N.332, A:K.498, A:Q.582 Salt bridges: A:K.498, A:K.498, A:K.533 pi-Stacking: A:Y.329 ADP.5: 25 residues within 4Å: Chain B: D.318, Y.329, E.330, K.498, L.515, A.531, K.533, G.537, R.538, C.539, G.540, I.543, L.545, Q.568, Q.569, L.570, W.571, C.572, L.573, Q.582, L.603, V.604, I.605 Ligands: MG.6, MG.7 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:D.318, B:K.533, B:G.537, B:C.539, B:G.540, B:Q.568, B:Q.569, B:W.571, B:I.605 Water bridges: B:Q.582, B:Q.582 Salt bridges: B:K.498, B:K.498, B:K.533

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: E.330, N.332, K.498 Ligands: ADP.2, MG.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.330, A:E.330, H2O.1, H2O.1 MG.4: 4 residues within 4Å: Chain A: D.318, E.330 Ligands: ADP.2, MG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.318, A:E.330, H2O.1, H2O.1 MG.6: 4 residues within 4Å: Chain B: E.330, N.332 Ligands: ADP.5, MG.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.330, B:E.330, H2O.5, H2O.5 MG.7: 4 residues within 4Å: Chain B: D.318, E.330 Ligands: ADP.5, MG.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.318, B:E.330, H2O.5, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pai, C.-H. et al., Structure and mechanism of Escherichia coli glutathionylspermidine amidase belonging to the family of cysteine; histidine-dependent amidohydrolases/peptidases. Protein Sci. (2011)

Release Date

2011-03-02

Peptides

Bifunctional glutathionylspermidine synthetase/amidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional glutathionylspermidine synthetase/amidase