SMTL ID : 2qc8.1

Crystal structure of human glutamine synthetase in complex with ADP and methionine sulfoximine phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-10-mer

Ligands

30 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: E.155, E.215, E.222 Ligands: MN.3, P3S.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.155, A:E.215, A:E.222, H2O.1 MN.2: 8 residues within 4Å: Chain A: E.153, H.272, R.343, E.357, R.359 Ligands: MN.3, ADP.5, P3S.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.153, A:E.153, A:H.272, A:E.357 MN.3: 6 residues within 4Å: Chain A: E.153, E.222 Ligands: MN.1, MN.2, ADP.5, P3S.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.153, A:E.222, H2O.1 MN.7: 5 residues within 4Å: Chain B: E.155, E.215, E.222 Ligands: MN.9, P3S.13 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.155, B:E.215, B:E.222, H2O.3 MN.8: 8 residues within 4Å: Chain B: E.153, H.272, R.343, E.357, R.359 Ligands: MN.9, ADP.12, P3S.13 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.153, B:E.153, B:H.272, B:E.357 MN.9: 6 residues within 4Å: Chain B: E.153, E.222 Ligands: MN.7, MN.8, ADP.12, P3S.13 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.153, B:E.222, H2O.3 MN.14: 5 residues within 4Å: Chain C: E.155, E.215, E.222 Ligands: MN.16, P3S.19 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.155, C:E.215, C:E.222, H2O.5 MN.15: 7 residues within 4Å: Chain C: E.153, H.272, E.357, R.359 Ligands: MN.16, ADP.18, P3S.19 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.153, C:E.153, C:H.272, C:E.357 MN.16: 6 residues within 4Å: Chain C: E.153, E.222 Ligands: MN.14, MN.15, ADP.18, P3S.19 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.153, C:E.222, H2O.5 MN.20: 5 residues within 4Å: Chain D: E.155, E.215, E.222 Ligands: MN.22, P3S.25 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.155, D:E.215, D:E.222 MN.21: 7 residues within 4Å: Chain D: E.153, H.272, E.357, R.359 Ligands: MN.22, ADP.24, P3S.25 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.153, D:E.153, D:H.272, D:E.357 MN.22: 7 residues within 4Å: Chain D: E.153, E.222, Q.224 Ligands: MN.20, MN.21, ADP.24, P3S.25 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.153, D:E.222, H2O.6 MN.26: 5 residues within 4Å: Chain E: E.155, E.215, E.222 Ligands: MN.28, P3S.30 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.155, E:E.215, E:E.222, H2O.8 MN.27: 7 residues within 4Å: Chain E: E.153, H.272, E.357, R.359 Ligands: MN.28, ADP.29, P3S.30 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:E.153, E:E.153, E:H.272, E:E.357 MN.28: 6 residues within 4Å: Chain E: E.153, E.222 Ligands: MN.26, MN.27, ADP.29, P3S.30 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.153, E:E.222, H2O.7 MN.31: 6 residues within 4Å: Chain F: E.153, E.155, E.215, E.222 Ligands: MN.33, P3S.36 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.155, F:E.215, F:E.222 MN.32: 8 residues within 4Å: Chain F: E.153, H.272, R.343, E.357, R.359 Ligands: MN.33, ADP.35, P3S.36 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:E.153, F:E.153, F:H.272, F:E.357 MN.33: 7 residues within 4Å: Chain F: E.153, E.222, Q.224 Ligands: MN.31, MN.32, ADP.35, P3S.36 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.153, F:E.222, H2O.8 MN.37: 6 residues within 4Å: Chain G: E.153, E.155, E.215, E.222 Ligands: MN.39, P3S.43 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.155, G:E.215, G:E.222 MN.38: 8 residues within 4Å: Chain G: E.153, H.272, R.343, E.357, R.359 Ligands: MN.39, ADP.42, P3S.43 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:E.153, G:E.153, G:H.272, G:E.357 MN.39: 7 residues within 4Å: Chain G: E.153, E.222, Q.224 Ligands: MN.37, MN.38, ADP.42, P3S.43 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:E.153, G:E.222 MN.44: 6 residues within 4Å: Chain H: E.153, E.155, E.215, E.222 Ligands: MN.46, P3S.48 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.155, H:E.215, H:E.222, H2O.9 MN.45: 7 residues within 4Å: Chain H: E.153, H.272, E.357, R.359 Ligands: MN.46, ADP.47, P3S.48 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:E.153, H:E.153, H:H.272, H:E.357 MN.46: 6 residues within 4Å: Chain H: E.153, E.222 Ligands: MN.44, MN.45, ADP.47, P3S.48 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.153, H:E.222, H2O.9 MN.49: 6 residues within 4Å: Chain I: E.153, E.155, E.215, E.222 Ligands: MN.51, P3S.54 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:E.155, I:E.215, I:E.222 MN.50: 8 residues within 4Å: Chain I: E.153, H.272, R.343, E.357, R.359 Ligands: MN.51, ADP.53, P3S.54 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:E.153, I:E.153, I:H.272, I:E.357 MN.51: 7 residues within 4Å: Chain I: E.153, E.222, Q.224 Ligands: MN.49, MN.50, ADP.53, P3S.54 3 PLIP interactions: 2 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:E.153, I:E.222, H2O.9 MN.55: 5 residues within 4Å: Chain J: E.155, E.215, E.222 Ligands: MN.57, P3S.60 4 PLIP interactions: 3 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:E.155, J:E.215, J:E.222, H2O.9 MN.56: 7 residues within 4Å: Chain J: E.153, H.272, R.343, E.357 Ligands: MN.57, ADP.59, P3S.60 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:E.153, J:E.153, J:H.272, J:E.357 MN.57: 6 residues within 4Å: Chain J: E.153, E.222 Ligands: MN.55, MN.56, ADP.59, P3S.60 3 PLIP interactions: 2 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:E.153, J:E.222, H2O.9

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

CL.4: 4 residues within 4Å: Chain A: T.212 Chain E: M.48, K.62, T.63 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: M.48, K.62, T.63 Chain C: T.212 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: M.48, K.62, T.63 Chain B: T.212 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain C: M.48, K.62, T.63, R.109 Chain D: T.212 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain D: M.48, K.62, T.63 Chain E: T.212 Ligand excluded by PLIP CL.34: 4 residues within 4Å: Chain F: T.212 Chain J: M.48, K.62, T.63 Ligand excluded by PLIP CL.40: 4 residues within 4Å: Chain F: M.48, K.62, T.63 Chain G: T.212 Ligand excluded by PLIP CL.41: 4 residues within 4Å: Chain G: M.48, K.62, T.63 Chain H: T.212 Ligand excluded by PLIP CL.52: 4 residues within 4Å: Chain H: M.48, K.62, T.63 Chain I: T.212 Ligand excluded by PLIP CL.58: 4 residues within 4Å: Chain I: M.48, K.62, T.63 Chain J: T.212 Ligand excluded by PLIP

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

ADP.5: 20 residues within 4Å: Chain A: W.149, F.150, G.151, E.153, A.210, E.222, Q.224, I.225, G.226, P.227, N.274, S.276, R.281, R.338, R.343, Y.355, E.357 Ligands: MN.2, MN.3, P3S.6 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.276, A:S.276 Water bridges: A:Q.224, A:Q.224, A:R.343, A:R.343 Salt bridges: A:R.338, A:R.343 pi-Stacking: A:Y.355, A:Y.355 ADP.12: 21 residues within 4Å: Chain B: W.149, F.150, G.151, E.153, A.210, E.222, Q.224, I.225, G.226, P.227, N.274, F.275, S.276, R.281, R.338, R.343, Y.355, E.357 Ligands: MN.8, MN.9, P3S.13 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.276, B:S.276 Water bridges: B:Q.224, B:Q.224, B:R.343, B:R.343 Salt bridges: B:R.338, B:R.343 ADP.18: 20 residues within 4Å: Chain C: W.149, F.150, G.151, E.153, A.210, E.222, Q.224, G.226, P.227, N.274, F.275, S.276, R.281, R.338, R.343, Y.355, E.357 Ligands: MN.15, MN.16, P3S.19 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.274, C:S.276, C:S.276, C:E.357, B:N.80 Water bridges: C:R.343, C:R.343 Salt bridges: C:R.338, C:R.343 pi-Stacking: C:Y.355, C:Y.355 ADP.24: 20 residues within 4Å: Chain D: W.149, F.150, G.151, E.153, A.210, E.222, Q.224, I.225, G.226, P.227, N.274, S.276, R.281, R.338, R.343, Y.355, E.357 Ligands: MN.21, MN.22, P3S.25 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.274, D:S.276, D:S.276 Water bridges: D:Q.224 Salt bridges: D:R.338, D:R.343, C:K.62 pi-Stacking: D:Y.355, D:Y.355 ADP.29: 20 residues within 4Å: Chain E: W.149, F.150, G.151, E.153, A.210, E.222, Q.224, I.225, G.226, P.227, N.274, S.276, R.281, R.338, R.343, Y.355, E.357 Ligands: MN.27, MN.28, P3S.30 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:N.274, E:S.276, E:S.276 Water bridges: E:R.343, E:R.343 Salt bridges: E:R.338, E:R.343, D:K.62 ADP.35: 21 residues within 4Å: Chain F: W.149, F.150, G.151, E.153, A.210, E.222, Q.224, I.225, G.226, P.227, N.274, F.275, S.276, R.281, R.338, R.343, Y.355, E.357 Ligands: MN.32, MN.33, P3S.36 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain J Hydrogen bonds: F:Q.224, F:N.274, F:S.276, F:S.276 Water bridges: F:R.343, F:R.343 Salt bridges: F:R.338, F:R.343, J:K.62 pi-Stacking: F:Y.355, F:Y.355 ADP.42: 19 residues within 4Å: Chain G: W.149, G.151, E.153, A.210, E.222, Q.224, I.225, G.226, P.227, N.274, S.276, R.281, R.338, R.343, Y.355, E.357 Ligands: MN.38, MN.39, P3S.43 6 PLIP interactions: 1 interactions with chain F, 5 interactions with chain G Salt bridges: F:K.62, G:R.338, G:R.343 Hydrogen bonds: G:N.274, G:S.276, G:S.276 ADP.47: 20 residues within 4Å: Chain H: W.149, F.150, G.151, E.153, A.210, E.222, Q.224, I.225, G.226, P.227, N.274, S.276, R.281, R.338, R.343, Y.355, E.357 Ligands: MN.45, MN.46, P3S.48 8 PLIP interactions: 2 interactions with chain G, 6 interactions with chain H Hydrogen bonds: G:N.80, H:N.274, H:S.276, H:S.276, H:E.357 Salt bridges: G:K.62, H:R.338, H:R.343 ADP.53: 21 residues within 4Å: Chain I: W.149, F.150, G.151, E.153, A.210, E.222, Q.224, I.225, G.226, P.227, N.274, F.275, S.276, R.281, R.338, R.343, Y.355, E.357 Ligands: MN.50, MN.51, P3S.54 8 PLIP interactions: 7 interactions with chain I, 1 interactions with chain H Hydrogen bonds: I:N.274, I:S.276, I:S.276 Water bridges: I:R.343, I:R.343 Salt bridges: I:R.338, I:R.343, H:K.62 ADP.59: 21 residues within 4Å: Chain J: W.149, F.150, G.151, M.152, E.153, A.210, E.222, Q.224, I.225, G.226, P.227, N.274, S.276, R.281, R.338, R.343, Y.355, E.357 Ligands: MN.56, MN.57, P3S.60 7 PLIP interactions: 5 interactions with chain J, 2 interactions with chain I Hydrogen bonds: J:N.274, J:S.276, J:S.276, I:N.80 Salt bridges: J:R.338, J:R.343, I:K.62

10 x P3S: L-METHIONINE-S-SULFOXIMINE PHOSPHATE(Non-covalent)

P3S.6: 23 residues within 4Å: Chain A: E.153, E.155, Y.181, E.215, V.216, E.222, N.267, G.268, G.270, H.272, R.318, H.323, E.324, T.325, R.338, E.357, R.359 Chain E: D.82, S.85 Ligands: MN.1, MN.2, MN.3, ADP.5 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.155, A:N.267, A:G.268, A:R.338, A:R.359, A:R.359 Salt bridges: A:H.272, A:R.318 P3S.13: 21 residues within 4Å: Chain A: D.82 Chain B: E.153, E.155, Y.181, E.215, V.216, E.222, N.267, G.268, H.272, R.318, H.323, E.324, T.325, R.338, E.357, R.359 Ligands: MN.7, MN.8, MN.9, ADP.12 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.155, B:N.267, B:G.268, B:R.338, B:R.359, B:R.359 Water bridges: B:G.268 Salt bridges: B:H.272, B:R.318 P3S.19: 19 residues within 4Å: Chain B: D.82 Chain C: E.153, E.155, Y.181, E.215, E.222, G.268, G.270, H.272, R.318, E.324, T.325, R.338, E.357, R.359 Ligands: MN.14, MN.15, MN.16, ADP.18 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:E.155, C:E.155, C:E.215, C:G.268, C:H.272, C:R.338, C:R.359, C:R.359 Water bridges: C:G.268 Salt bridges: C:H.272, C:R.318 P3S.25: 19 residues within 4Å: Chain C: D.82 Chain D: E.153, E.155, Y.181, E.215, E.222, G.268, H.272, R.318, H.323, E.324, T.325, R.338, E.357, R.359 Ligands: MN.20, MN.21, MN.22, ADP.24 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:E.155, D:G.268, D:R.338, D:R.343, D:R.359, D:R.359 Water bridges: D:Q.220 Salt bridges: D:H.272, D:R.318 P3S.30: 19 residues within 4Å: Chain D: D.82 Chain E: E.153, E.155, Y.181, E.215, E.222, G.268, H.272, R.318, H.323, E.324, T.325, R.338, E.357, R.359 Ligands: MN.26, MN.27, MN.28, ADP.29 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:E.155, E:N.267, E:G.268, E:R.338, E:R.343, E:R.359, E:R.359 Salt bridges: E:H.272, E:R.318 P3S.36: 19 residues within 4Å: Chain F: E.153, E.155, Y.181, E.215, E.222, N.267, G.268, H.272, R.318, E.324, T.325, R.338, E.357, R.359 Chain J: D.82 Ligands: MN.31, MN.32, MN.33, ADP.35 9 PLIP interactions: 8 interactions with chain F, 1 interactions with chain J Hydrogen bonds: F:E.155, F:G.268, F:R.338, F:R.359, F:R.359, J:D.82 Water bridges: F:N.267 Salt bridges: F:H.272, F:R.318 P3S.43: 22 residues within 4Å: Chain F: D.82 Chain G: E.153, E.155, Y.181, E.215, V.216, E.222, N.267, G.268, G.270, H.272, R.318, H.323, E.324, T.325, R.338, E.357, R.359 Ligands: MN.37, MN.38, MN.39, ADP.42 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:E.155, G:N.267, G:G.268, G:G.270, G:R.338, G:R.359, G:R.359 Salt bridges: G:H.272, G:R.318 P3S.48: 21 residues within 4Å: Chain G: D.82 Chain H: E.153, E.155, Y.181, E.215, E.222, N.267, G.268, G.270, H.272, R.318, H.323, E.324, T.325, R.338, E.357, R.359 Ligands: MN.44, MN.45, MN.46, ADP.47 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:E.155, H:N.267, H:G.268, H:R.338, H:R.343, H:R.359, H:R.359 Salt bridges: H:H.272, H:R.318 P3S.54: 23 residues within 4Å: Chain H: D.82 Chain I: E.153, E.155, Y.181, E.215, E.222, N.267, G.268, A.269, G.270, H.272, R.318, H.323, E.324, T.325, R.338, R.343, E.357, R.359 Ligands: MN.49, MN.50, MN.51, ADP.53 9 PLIP interactions: 9 interactions with chain I Hydrogen bonds: I:E.155, I:N.267, I:G.268, I:R.338, I:R.343, I:R.359, I:R.359 Salt bridges: I:H.272, I:R.318 P3S.60: 22 residues within 4Å: Chain I: D.82 Chain J: E.153, E.155, Y.181, E.215, V.216, E.222, N.267, G.268, H.272, R.318, H.323, E.324, T.325, R.338, R.343, E.357, R.359 Ligands: MN.55, MN.56, MN.57, ADP.59 10 PLIP interactions: 10 interactions with chain J Hydrogen bonds: J:E.155, J:G.270, J:H.323, J:R.338, J:R.343, J:R.359, J:R.359 Water bridges: J:N.267 Salt bridges: J:H.272, J:R.318

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krajewski, W.W. et al., Crystal structures of mammalian glutamine synthetases illustrate substrate-induced conformational changes and provide opportunities for drug and herbicide design. J.Mol.Biol. (2008)

Release Date

2007-07-03

Peptides

Glutamine synthetase: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

Glutamine synthetase

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