SMTL ID : 2d32.1 (1 other biounit)

Crystal Structure of Michaelis Complex of gamma-Glutamylcysteine Synthetase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

13 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: E.29, D.60, E.67 Ligands: GLU.5, CYS.6, ANP.7 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:E.29, A:D.60, A:E.67, GLU.5, H2O.8 MG.2: 5 residues within 4Å: Chain A: E.27, H.150, E.328 Ligands: MG.3, ANP.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.27, A:E.27, A:H.150, A:E.328 MG.3: 5 residues within 4Å: Chain A: E.27, E.67, I.69 Ligands: MG.2, ANP.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.27, A:E.67, H2O.10 MG.4: 2 residues within 4Å: Chain A: N.442, D.444 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.444, H2O.3, H2O.8, H2O.12 MG.8: 5 residues within 4Å: Chain B: E.29, D.60, E.67 Ligands: GLU.11, ANP.13 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:E.29, B:D.60, B:E.67, GLU.11, H2O.16 MG.9: 5 residues within 4Å: Chain B: E.27, H.150, E.328 Ligands: MG.10, ANP.13 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.27, B:E.27, B:H.150, B:E.328 MG.10: 5 residues within 4Å: Chain B: E.27, E.67, I.69 Ligands: MG.9, ANP.13 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.27, B:E.67 MG.14: 5 residues within 4Å: Chain C: E.29, D.60, E.67 Ligands: GLU.17, ANP.19 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.29, C:D.60, C:E.67, H2O.23 MG.15: 4 residues within 4Å: Chain C: E.27, H.150, E.328 Ligands: ANP.19 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.27, C:E.27, C:H.150, C:E.328 MG.16: 4 residues within 4Å: Chain C: E.27, E.67, I.69 Ligands: ANP.19 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.27, C:E.67 MG.20: 6 residues within 4Å: Chain D: E.29, D.60, E.67 Ligands: GLU.23, CYS.24, ANP.25 5 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: D:E.29, D:D.60, D:E.67, GLU.23, H2O.24 MG.21: 5 residues within 4Å: Chain D: E.27, H.150, E.328 Ligands: MG.22, ANP.25 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.27, D:E.27, D:H.150, D:E.328 MG.22: 5 residues within 4Å: Chain D: E.27, E.67, I.69 Ligands: MG.21, ANP.25 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.27, D:E.67, H2O.31

4 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.5: 11 residues within 4Å: Chain A: E.29, D.60, I.146, S.147, G.148, H.150, R.235, R.330 Ligands: MG.1, CYS.6, ANP.7 8 PLIP interactions: 6 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:I.146, A:H.150, C.6 Water bridges: A:R.304, E.5 Salt bridges: A:H.150, A:R.235, A:R.330 GLU.11: 12 residues within 4Å: Chain B: E.29, D.60, I.146, S.147, G.148, H.150, R.235, Y.241, R.330 Ligands: MG.8, CYS.12, ANP.13 9 PLIP interactions: 8 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.241 Hydrogen bonds: B:I.146, C.12 Water bridges: B:Y.241, B:R.330 Salt bridges: B:H.150, B:H.150, B:R.235, B:R.330 GLU.17: 12 residues within 4Å: Chain C: E.29, D.60, I.146, S.147, G.148, H.150, R.235, Y.241, R.330 Ligands: MG.14, CYS.18, ANP.19 10 PLIP interactions: 9 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:Y.241 Hydrogen bonds: C:I.146, C:H.150, C:Y.241, C.18 Water bridges: C:E.29, C:Y.241 Salt bridges: C:H.150, C:R.235, C:R.330 GLU.23: 12 residues within 4Å: Chain D: E.29, D.60, I.146, S.147, G.148, H.150, R.235, Y.241, R.330 Ligands: MG.20, CYS.24, ANP.25 8 PLIP interactions: 1 Ligand-Ligand interactions, 7 interactions with chain D Hydrogen bonds: C.24, D:I.146, D:H.150 Hydrophobic interactions: D:Y.241 Water bridges: D:R.330 Salt bridges: D:H.150, D:R.235, D:R.330

4 x CYS: CYSTEINE(Non-covalent)

CYS.6: 8 residues within 4Å: Chain A: D.60, F.61, Y.131, R.132, L.135, N.297 Ligands: MG.1, GLU.5 7 PLIP interactions: 5 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:D.60, A:Y.131, A:N.297, C.6, C.6 Water bridges: A:R.330, A:R.330 CYS.12: 9 residues within 4Å: Chain B: D.60, F.61, Y.131, R.132, L.135, Q.144, Y.241, N.297 Ligands: GLU.11 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:D.60, C.12, C.12 Water bridges: B:R.304, B:R.304 CYS.18: 9 residues within 4Å: Chain C: D.60, F.61, Y.131, R.132, L.135, Y.241, N.297 Ligands: GLU.17, ANP.19 4 PLIP interactions: 2 Ligand-Ligand interactions, 2 interactions with chain C Hydrogen bonds: C.18, C.18, C:D.60, C:N.297 CYS.24: 10 residues within 4Å: Chain D: D.60, F.61, Y.131, R.132, L.135, Y.241, N.297 Ligands: MG.20, GLU.23, ANP.25 4 PLIP interactions: 2 Ligand-Ligand interactions, 2 interactions with chain D Hydrogen bonds: C.24, C.24, D:D.60 Water bridges: D:R.304

4 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.7: 24 residues within 4Å: Chain A: Q.23, G.25, L.26, E.27, E.67, I.69, T.70, P.71, V.72, H.150, N.152, F.153, S.154, N.297, K.306, V.308, E.325, Y.326, E.328, R.330 Ligands: MG.1, MG.2, MG.3, GLU.5 14 PLIP interactions: 2 Ligand-Ligand interactions, 12 interactions with chain A Hydrogen bonds: C.6, C.6, A:L.26, A:T.70, A:N.152, A:S.154, A:K.306, A:K.306, A:E.325, A:R.330 Water bridges: A:V.72, A:R.330 pi-Stacking: A:Y.326, A:Y.326 ANP.13: 24 residues within 4Å: Chain B: Q.23, R.24, G.25, L.26, E.27, E.67, I.69, T.70, P.71, V.72, H.150, N.152, F.153, S.154, N.297, K.306, V.308, E.325, Y.326, E.328 Ligands: MG.8, MG.9, MG.10, GLU.11 17 PLIP interactions: 15 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:L.26, B:T.70, B:H.150, B:N.152, B:S.154, B:K.306, B:K.306, B:E.325, B:E.325, C.12, C.12 Water bridges: B:V.72, B:R.304, B:R.330, B:R.330 pi-Stacking: B:Y.326, B:Y.326 ANP.19: 22 residues within 4Å: Chain C: Q.23, R.24, G.25, L.26, E.27, E.67, I.69, T.70, P.71, V.72, N.152, F.153, S.154, K.306, E.325, Y.326, E.328 Ligands: MG.14, MG.15, MG.16, GLU.17, CYS.18 14 PLIP interactions: 12 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: C:L.26, C:T.70, C:N.152, C:S.154, C:K.306, C:K.306, C:E.325, C:E.325, C:Y.326, C.18, C.18 Water bridges: C:E.29 pi-Stacking: C:Y.326, C:Y.326 ANP.25: 25 residues within 4Å: Chain D: Q.23, R.24, G.25, L.26, E.27, E.67, I.69, T.70, P.71, V.72, H.150, N.152, F.153, S.154, N.297, K.306, V.308, E.325, Y.326, E.328 Ligands: MG.20, MG.21, MG.22, GLU.23, CYS.24 20 PLIP interactions: 17 interactions with chain D, 3 Ligand-Ligand interactions Hydrogen bonds: D:L.26, D:T.70, D:H.150, D:N.152, D:S.154, D:K.306, D:K.306, D:E.325, D:E.325, D:Y.326, D:R.330, C.24, C.24, C.24 Water bridges: D:D.60, D:V.72, D:R.304, D:R.304 pi-Stacking: D:Y.326, D:Y.326

Links

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Citation

Hibi, T. et al., Structural basis of efficient coupling peptide ligation and ATP hydrolysis by gamma-gluatamylcysteine synthetase. To be Published

Release Date

2006-11-14

Peptides

Glutamate--cysteine ligase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glutamate--cysteine ligase

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