SMTL ID : 3kal.1

Structure of homoglutathione synthetase from Glycine max in closed conformation with homoglutathione, ADP, a sulfate ion, and three magnesium ions bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 22 residues within 4Å: Chain A: M.157, I.168, E.169, K.334, V.386, K.388, R.391, E.392, G.393, G.394, N.396, N.397, Y.399, M.424, Q.425, R.426, I.427, E.450, K.477 Ligands: MG.3, MG.4, SO4.6 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:E.169, A:K.388, A:G.393, A:G.394, A:N.396, A:N.397, A:Y.399, A:Q.425, A:I.427, A:E.450, A:K.477 Water bridges: A:K.334, A:E.450, A:E.450, A:E.450, A:R.475, A:R.475 Salt bridges: A:K.334, A:K.334, A:K.388 ADP.8: 22 residues within 4Å: Chain B: M.157, I.168, E.169, K.334, V.386, K.388, R.391, E.392, G.393, G.394, N.396, N.397, Y.399, M.424, Q.425, R.426, I.427, E.450, K.477 Ligands: MG.10, MG.11, SO4.13 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:K.388, B:G.393, B:G.394, B:N.396, B:N.397, B:Q.425, B:I.427, B:E.450, B:K.477 Water bridges: B:K.334, B:Y.399, B:R.475, B:R.475, B:R.475 Salt bridges: B:K.334, B:K.334, B:K.388

4 x HGS: D-gamma-glutamyl-L-cysteinyl-beta-alanine(Non-covalent)

HGS.2: 19 residues within 4Å: Chain A: R.153, N.171, I.173, S.174, T.175, S.176, F.177, Q.238, E.241, N.243, R.295, Y.298, E.392, R.475, G.485, V.486, L.487, P.488 Ligands: SO4.6 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.177, A:Y.298 Hydrogen bonds: A:R.153, A:R.153, A:S.174, A:S.176, A:S.176, A:E.241, A:N.243, A:R.295, A:R.475, A:V.486, A:L.487 Water bridges: A:Q.238, A:R.295, A:R.295 Salt bridges: A:R.295, A:R.475 HGS.7: 9 residues within 4Å: Chain A: W.49, N.53, C.182, L.183, G.186, N.209, N.210, V.212, D.213 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.49 Hydrogen bonds: A:D.213 Water bridges: A:G.186, A:N.209, A:N.209, A:Y.249 HGS.9: 17 residues within 4Å: Chain B: R.153, N.171, I.173, S.174, T.175, S.176, F.177, Q.238, E.241, N.243, R.295, Y.298, E.392, R.475, G.485, V.486 Ligands: SO4.13 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.298 Hydrogen bonds: B:R.153, B:R.153, B:S.174, B:S.176, B:E.241, B:E.241, B:N.243, B:Y.298, B:R.475, B:V.486 Water bridges: B:Q.238, B:E.241, B:R.295 Salt bridges: B:R.295, B:R.475 HGS.14: 7 residues within 4Å: Chain B: W.49, N.53, C.182, L.183, V.212, D.213, Y.249 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.49 Hydrogen bonds: B:C.182 Water bridges: B:W.49, B:G.186, B:N.209, B:Y.249, B:Y.249

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 6 residues within 4Å: Chain A: E.169, N.171, E.392 Ligands: ADP.1, MG.4, SO4.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.169, A:E.169, A:E.392 MG.4: 4 residues within 4Å: Chain A: E.169 Ligands: ADP.1, MG.3, SO4.6 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.169, H2O.4, H2O.8 MG.5: 5 residues within 4Å: Chain A: E.169, M.170, N.171, G.332, E.392 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:M.170, A:G.332, A:E.392, H2O.3, H2O.5 MG.10: 7 residues within 4Å: Chain B: E.169, N.171, K.334, E.392 Ligands: ADP.8, MG.11, SO4.13 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.169, B:E.169, B:E.392 MG.11: 5 residues within 4Å: Chain B: D.155, E.169 Ligands: ADP.8, MG.10, SO4.13 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.169, H2O.19, H2O.21 MG.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 11 residues within 4Å: Chain A: R.153, D.155, E.169, N.171, E.392, G.393, R.475 Ligands: ADP.1, HGS.2, MG.3, MG.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.169, A:N.171 Water bridges: A:R.475 Salt bridges: A:R.153, A:R.475 SO4.13: 12 residues within 4Å: Chain B: R.153, D.155, E.169, N.171, E.392, G.393, G.394, R.475 Ligands: ADP.8, HGS.9, MG.10, MG.11 3 PLIP interactions: 3 interactions with chain B Water bridges: B:D.155 Salt bridges: B:R.153, B:R.475

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Galant, A. et al., Structural Basis for Evolution of Product Diversity in Soybean Glutathione Biosynthesis. Plant Cell (2009)

Release Date

2009-12-22

Peptides

homoglutathione synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

homoglutathione synthetase

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