SMTL ID : 2d33.1

Crystal Structure of gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 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: MG.3, GLU.5, AF3.8 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.7 MG.2: 6 residues within 4Å: Chain A: E.27, H.150, E.328 Ligands: MG.3, ADP.7, AF3.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.27, A:E.27, A:H.150, A:E.328 MG.3: 6 residues within 4Å: Chain A: E.27, E.67 Ligands: MG.1, MG.2, ADP.7, AF3.8 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.27, A:E.67, H2O.2 MG.4: 2 residues within 4Å: Chain A: N.442, D.444 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.444, H2O.3, H2O.3 MG.9: 6 residues within 4Å: Chain B: E.29, D.60, E.67 Ligands: MG.11, GLU.12, AF3.15 5 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: GLU.12, B:E.29, B:D.60, B:E.67, H2O.10 MG.10: 8 residues within 4Å: Chain B: E.27, H.150, E.328, R.330 Ligands: MG.11, GLU.12, ADP.14, AF3.15 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.27, B:E.27, B:H.150, B:E.328 MG.11: 6 residues within 4Å: Chain B: E.27, E.67 Ligands: MG.9, MG.10, ADP.14, AF3.15 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.27, B:E.67, H2O.10 MG.16: 6 residues within 4Å: Chain C: E.29, D.60, E.67 Ligands: MG.18, GLU.19, AF3.22 5 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: GLU.19, C:E.29, C:D.60, C:E.67, H2O.11 MG.17: 6 residues within 4Å: Chain C: E.27, H.150, E.328 Ligands: MG.18, ADP.21, AF3.22 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.27, C:E.27, C:H.150, C:E.328 MG.18: 6 residues within 4Å: Chain C: E.27, E.67 Ligands: MG.16, MG.17, ADP.21, AF3.22 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.27, C:E.67 MG.23: 7 residues within 4Å: Chain D: E.29, D.60, E.67 Ligands: MG.25, GLU.26, CYS.27, AF3.29 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.26, H2O.13 MG.24: 7 residues within 4Å: Chain D: E.27, H.150, E.328, R.330 Ligands: MG.25, ADP.28, AF3.29 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.27, D:E.27, D:H.150, D:E.328 MG.25: 6 residues within 4Å: Chain D: E.27, E.67 Ligands: MG.23, MG.24, ADP.28, AF3.29 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.27, D:E.67, H2O.12

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, AF3.8 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:I.146, A:H.150, C.6 Salt bridges: A:H.150, A:R.235, A:R.330 GLU.12: 13 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.9, MG.10, CYS.13, AF3.15 8 PLIP interactions: 7 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:I.146, C.13 Water bridges: B:Y.241, B:R.330 Salt bridges: B:H.150, B:H.150, B:R.235, B:R.330 GLU.19: 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.16, CYS.20, AF3.22 8 PLIP interactions: 7 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:Y.241 Hydrogen bonds: C:E.29, C:I.146, C.20 Salt bridges: C:H.150, C:H.150, C:R.235, C:R.330 GLU.26: 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.23, CYS.27, AF3.29 7 PLIP interactions: 6 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: D:I.146, C.27 Water bridges: D:E.29 Salt bridges: D:H.150, 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: GLU.5, AF3.8 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:D.60, A:Y.131, A:N.297, C.6, C.6 CYS.13: 11 residues within 4Å: Chain B: D.60, F.61, Y.131, R.132, L.135, Q.144, Y.241, N.297, Y.300 Ligands: GLU.12, AF3.15 5 PLIP interactions: 2 Ligand-Ligand interactions, 3 interactions with chain B Hydrogen bonds: C.13, C.13, B:D.60, B:N.297 Water bridges: B:R.330 CYS.20: 11 residues within 4Å: Chain C: D.60, F.61, Y.131, R.132, L.135, Q.144, Y.241, N.297, Y.300 Ligands: GLU.19, AF3.22 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: C:D.60, C:N.297, C.20, C.20 CYS.27: 12 residues within 4Å: Chain D: D.60, F.61, Y.131, R.132, L.135, Q.144, Y.241, N.297, Y.300 Ligands: MG.23, GLU.26, AF3.29 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: D:D.60, D:N.297, C.27, C.27

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

ADP.7: 21 residues within 4Å: Chain A: 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, V.308, E.325, Y.326, E.328 Ligands: MG.2, MG.3, AF3.8 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:L.26, A:T.70, A:N.152, A:S.154, A:E.325 Water bridges: A:E.67, A:K.306, A:K.306 Salt bridges: A:K.306 pi-Stacking: A:Y.326, A:Y.326 ADP.14: 20 residues within 4Å: Chain B: Q.23, G.25, L.26, E.27, E.67, I.69, T.70, P.71, V.72, N.152, F.153, S.154, K.306, V.308, E.325, Y.326, E.328 Ligands: MG.10, MG.11, AF3.15 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:L.26, B:T.70, B:N.152, B:S.154, B:E.325, B:E.325 Salt bridges: B:K.306 pi-Stacking: B:Y.326, B:Y.326 ADP.21: 21 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, V.308, E.325, Y.326, E.328 Ligands: MG.17, MG.18, AF3.22 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:L.26, C:T.70, C:N.152, C:S.154, C:E.325, C:E.325 Water bridges: C:Y.326, C:Y.326 Salt bridges: C:K.306 pi-Stacking: C:Y.326, C:Y.326 ADP.28: 21 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, N.152, F.153, S.154, K.306, V.308, E.325, Y.326, E.328 Ligands: MG.24, MG.25, AF3.29 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:L.26, D:T.70, D:N.152, D:S.154, D:E.325 Water bridges: D:V.72, D:Y.326, D:Y.326 Salt bridges: D:K.306 pi-Stacking: D:Y.326, D:Y.326

4 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.8: 11 residues within 4Å: Chain A: E.27, D.60, E.67, H.150, R.330 Ligands: MG.1, MG.2, MG.3, GLU.5, CYS.6, ADP.7 No protein-ligand interaction detected (PLIP) AF3.15: 12 residues within 4Å: Chain B: E.27, D.60, E.67, H.150, E.328, R.330 Ligands: MG.9, MG.10, MG.11, GLU.12, CYS.13, ADP.14 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: GLU.12 AF3.22: 12 residues within 4Å: Chain C: E.27, D.60, E.67, H.150, E.328, R.330 Ligands: MG.16, MG.17, MG.18, GLU.19, CYS.20, ADP.21 No protein-ligand interaction detected (PLIP) AF3.29: 12 residues within 4Å: Chain D: E.27, D.60, E.67, H.150, E.328, R.330 Ligands: MG.23, MG.24, MG.25, GLU.26, CYS.27, ADP.28 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: GLU.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hibi, T. et al., Structural basis of efficient coupling between 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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