SMTL ID : 1f1h.1

CRYSTAL STRUCTURE OF GLUTAMINE SYNTHETASE FROM SALMONELLA TYPHIMURIUM WITH THALLIUM IONS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.67 Å

Oligo State

homo-12-mer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: E.131, E.212, E.220 Ligands: ADP.3, TL.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.131, A:E.212, A:E.220, H2O.3, H2O.4 MN.2: 4 residues within 4Å: Chain A: E.129, H.269, E.357 Ligands: ADP.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.129, A:E.129, A:H.269, A:E.357, H2O.4 MN.7: 5 residues within 4Å: Chain B: E.131, E.212, E.220 Ligands: ADP.9, TL.10 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.131, B:E.212, B:E.220, H2O.8, H2O.9 MN.8: 4 residues within 4Å: Chain B: E.129, H.269, E.357 Ligands: ADP.9 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.129, B:E.129, B:H.269, B:E.357, H2O.9 MN.13: 5 residues within 4Å: Chain C: E.131, E.212, E.220 Ligands: ADP.15, TL.16 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.131, C:E.212, C:E.220, H2O.13, H2O.15 MN.14: 4 residues within 4Å: Chain C: E.129, H.269, E.357 Ligands: ADP.15 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.129, C:E.129, C:H.269, C:E.357, H2O.14 MN.19: 5 residues within 4Å: Chain D: E.131, E.212, E.220 Ligands: ADP.21, TL.22 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.131, D:E.212, D:E.220, H2O.17, H2O.19 MN.20: 4 residues within 4Å: Chain D: E.129, H.269, E.357 Ligands: ADP.21 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.129, D:E.129, D:H.269, D:E.357, H2O.18 MN.25: 5 residues within 4Å: Chain E: E.131, E.212, E.220 Ligands: ADP.27, TL.28 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.131, E:E.212, E:E.220, H2O.22, H2O.23 MN.26: 4 residues within 4Å: Chain E: E.129, H.269, E.357 Ligands: ADP.27 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.129, E:E.129, E:H.269, E:E.357, H2O.23 MN.31: 5 residues within 4Å: Chain F: E.131, E.212, E.220 Ligands: ADP.33, TL.34 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.131, F:E.212, F:E.220, H2O.27, H2O.28 MN.32: 4 residues within 4Å: Chain F: E.129, H.269, E.357 Ligands: ADP.33 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.129, F:E.129, F:H.269, F:E.357, H2O.28 MN.37: 5 residues within 4Å: Chain G: E.131, E.212, E.220 Ligands: ADP.39, TL.40 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.131, G:E.212, G:E.220, H2O.31, H2O.33 MN.38: 4 residues within 4Å: Chain G: E.129, H.269, E.357 Ligands: ADP.39 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.129, G:E.129, G:H.269, G:E.357, H2O.32 MN.43: 5 residues within 4Å: Chain H: E.131, E.212, E.220 Ligands: ADP.45, TL.46 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.131, H:E.212, H:E.220, H2O.36, H2O.37 MN.44: 4 residues within 4Å: Chain H: E.129, H.269, E.357 Ligands: ADP.45 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.129, H:E.129, H:H.269, H:E.357, H2O.37 MN.49: 5 residues within 4Å: Chain I: E.131, E.212, E.220 Ligands: ADP.51, TL.52 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:E.131, I:E.212, I:E.220, H2O.41, H2O.42 MN.50: 4 residues within 4Å: Chain I: E.129, H.269, E.357 Ligands: ADP.51 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:E.129, I:E.129, I:H.269, I:E.357, H2O.42 MN.55: 5 residues within 4Å: Chain J: E.131, E.212, E.220 Ligands: ADP.57, TL.58 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.131, J:E.212, J:E.220, H2O.45, H2O.46 MN.56: 4 residues within 4Å: Chain J: E.129, H.269, E.357 Ligands: ADP.57 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:E.129, J:E.129, J:H.269, J:E.357, H2O.46 MN.61: 5 residues within 4Å: Chain K: E.131, E.212, E.220 Ligands: ADP.63, TL.64 5 PLIP interactions: 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:E.131, K:E.212, K:E.220, H2O.50, H2O.51 MN.62: 4 residues within 4Å: Chain K: E.129, H.269, E.357 Ligands: ADP.63 5 PLIP interactions: 4 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:E.129, K:E.129, K:H.269, K:E.357, H2O.51 MN.67: 5 residues within 4Å: Chain L: E.131, E.212, E.220 Ligands: ADP.69, TL.70 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:E.131, L:E.212, L:E.220, H2O.55, H2O.56 MN.68: 4 residues within 4Å: Chain L: E.129, H.269, E.357 Ligands: ADP.69 5 PLIP interactions: 4 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:E.129, L:E.129, L:H.269, L:E.357, H2O.56

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

ADP.3: 15 residues within 4Å: Chain A: G.127, E.129, E.207, H.210, E.220, T.223, R.224, F.225, H.271, S.273, A.353, R.355 Chain B: D.50 Ligands: MN.1, MN.2 9 PLIP interactions: 1 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:D.50, A:E.207, A:F.225, A:S.273, A:S.273 Water bridges: A:E.220, A:T.223 Salt bridges: A:H.210 pi-Cation interactions: A:R.355 ADP.9: 15 residues within 4Å: Chain B: G.127, E.129, E.207, H.210, E.220, T.223, R.224, F.225, H.271, S.273, A.353, R.355 Chain C: D.50 Ligands: MN.7, MN.8 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:E.207, B:F.225, B:S.273, B:S.273, C:D.50 Water bridges: B:E.220, B:T.223 Salt bridges: B:H.210 pi-Cation interactions: B:R.355 ADP.15: 15 residues within 4Å: Chain C: G.127, E.129, E.207, H.210, E.220, T.223, R.224, F.225, H.271, S.273, A.353, R.355 Chain D: D.50 Ligands: MN.13, MN.14 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.207, C:F.225, C:S.273, C:S.273, D:D.50 Water bridges: C:E.220, C:T.223 Salt bridges: C:H.210 pi-Cation interactions: C:R.355 ADP.21: 15 residues within 4Å: Chain D: G.127, E.129, E.207, H.210, E.220, T.223, R.224, F.225, H.271, S.273, A.353, R.355 Chain E: D.50 Ligands: MN.19, MN.20 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:E.207, D:F.225, D:S.273, D:S.273, E:D.50 Water bridges: D:E.220, D:T.223 Salt bridges: D:H.210 pi-Cation interactions: D:R.355 ADP.27: 15 residues within 4Å: Chain E: G.127, E.129, E.207, H.210, E.220, T.223, R.224, F.225, H.271, S.273, A.353, R.355 Chain F: D.50 Ligands: MN.25, MN.26 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:E.207, E:F.225, E:S.273, E:S.273, F:D.50 Water bridges: E:E.220, E:T.223 Salt bridges: E:H.210 pi-Cation interactions: E:R.355 ADP.33: 15 residues within 4Å: Chain A: D.50 Chain F: G.127, E.129, E.207, H.210, E.220, T.223, R.224, F.225, H.271, S.273, A.353, R.355 Ligands: MN.31, MN.32 9 PLIP interactions: 8 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:E.207, F:F.225, F:S.273, F:S.273, A:D.50 Water bridges: F:E.220, F:T.223 Salt bridges: F:H.210 pi-Cation interactions: F:R.355 ADP.39: 15 residues within 4Å: Chain G: G.127, E.129, E.207, H.210, E.220, T.223, R.224, F.225, H.271, S.273, A.353, R.355 Chain L: D.50 Ligands: MN.37, MN.38 9 PLIP interactions: 2 interactions with chain L, 7 interactions with chain G Hydrogen bonds: L:D.50, L:D.50, G:E.207, G:F.225, G:S.273, G:S.273 Water bridges: G:E.220 Salt bridges: G:H.210 pi-Cation interactions: G:R.355 ADP.45: 15 residues within 4Å: Chain G: D.50 Chain H: G.127, E.129, E.207, H.210, E.220, T.223, R.224, F.225, H.271, S.273, A.353, R.355 Ligands: MN.43, MN.44 13 PLIP interactions: 11 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:E.129, H:E.207, H:E.220, H:F.225, H:S.273, H:S.273, G:D.50, G:D.50 Water bridges: H:E.131, H:H.269, H:H.269 Salt bridges: H:H.210 pi-Cation interactions: H:R.355 ADP.51: 15 residues within 4Å: Chain H: D.50 Chain I: G.127, E.129, E.207, H.210, E.220, T.223, R.224, F.225, H.271, S.273, A.353, R.355 Ligands: MN.49, MN.50 9 PLIP interactions: 7 interactions with chain I, 2 interactions with chain H Hydrogen bonds: I:E.207, I:F.225, I:S.273, I:S.273, H:D.50, H:D.50 Water bridges: I:E.220 Salt bridges: I:H.210 pi-Cation interactions: I:R.355 ADP.57: 15 residues within 4Å: Chain I: D.50 Chain J: G.127, E.129, E.207, H.210, E.220, T.223, R.224, F.225, H.271, S.273, A.353, R.355 Ligands: MN.55, MN.56 9 PLIP interactions: 7 interactions with chain J, 2 interactions with chain I Hydrogen bonds: J:E.207, J:F.225, J:S.273, J:S.273, I:D.50, I:D.50 Water bridges: J:E.220 Salt bridges: J:H.210 pi-Cation interactions: J:R.355 ADP.63: 15 residues within 4Å: Chain J: D.50 Chain K: G.127, E.129, E.207, H.210, E.220, T.223, R.224, F.225, H.271, S.273, A.353, R.355 Ligands: MN.61, MN.62 9 PLIP interactions: 7 interactions with chain K, 2 interactions with chain J Hydrogen bonds: K:E.207, K:F.225, K:S.273, K:S.273, J:D.50, J:D.50 Water bridges: K:E.220 Salt bridges: K:H.210 pi-Cation interactions: K:R.355 ADP.69: 15 residues within 4Å: Chain K: D.50 Chain L: G.127, E.129, E.207, H.210, E.220, T.223, R.224, F.225, H.271, S.273, A.353, R.355 Ligands: MN.67, MN.68 10 PLIP interactions: 8 interactions with chain L, 2 interactions with chain K Hydrogen bonds: L:E.207, L:E.220, L:F.225, L:S.273, L:S.273, K:D.50, K:D.50 Water bridges: L:E.131 Salt bridges: L:H.210 pi-Cation interactions: L:R.355

24 x TL: THALLIUM (I) ION(Non-covalent)

TL.4: 5 residues within 4Å: Chain A: Y.179, E.212 Chain B: D.50, S.53 Ligands: MN.1 Ligand excluded by PLIP TL.5: 3 residues within 4Å: Chain A: E.131, N.264, G.265 Ligand excluded by PLIP TL.10: 5 residues within 4Å: Chain B: Y.179, E.212 Chain C: D.50, S.53 Ligands: MN.7 Ligand excluded by PLIP TL.11: 3 residues within 4Å: Chain B: E.131, N.264, G.265 Ligand excluded by PLIP TL.16: 5 residues within 4Å: Chain C: Y.179, E.212 Chain D: D.50, S.53 Ligands: MN.13 Ligand excluded by PLIP TL.17: 3 residues within 4Å: Chain C: E.131, N.264, G.265 Ligand excluded by PLIP TL.22: 5 residues within 4Å: Chain D: Y.179, E.212 Chain E: D.50, S.53 Ligands: MN.19 Ligand excluded by PLIP TL.23: 3 residues within 4Å: Chain D: E.131, N.264, G.265 Ligand excluded by PLIP TL.28: 5 residues within 4Å: Chain E: Y.179, E.212 Chain F: D.50, S.53 Ligands: MN.25 Ligand excluded by PLIP TL.29: 3 residues within 4Å: Chain E: E.131, N.264, G.265 Ligand excluded by PLIP TL.34: 5 residues within 4Å: Chain A: D.50, S.53 Chain F: Y.179, E.212 Ligands: MN.31 Ligand excluded by PLIP TL.35: 3 residues within 4Å: Chain F: E.131, N.264, G.265 Ligand excluded by PLIP TL.40: 5 residues within 4Å: Chain G: Y.179, E.212 Chain L: D.50, S.53 Ligands: MN.37 Ligand excluded by PLIP TL.41: 3 residues within 4Å: Chain G: E.131, N.264, G.265 Ligand excluded by PLIP TL.46: 5 residues within 4Å: Chain G: D.50, S.53 Chain H: Y.179, E.212 Ligands: MN.43 Ligand excluded by PLIP TL.47: 3 residues within 4Å: Chain H: E.131, N.264, G.265 Ligand excluded by PLIP TL.52: 5 residues within 4Å: Chain H: D.50, S.53 Chain I: Y.179, E.212 Ligands: MN.49 Ligand excluded by PLIP TL.53: 3 residues within 4Å: Chain I: E.131, N.264, G.265 Ligand excluded by PLIP TL.58: 5 residues within 4Å: Chain I: D.50, S.53 Chain J: Y.179, E.212 Ligands: MN.55 Ligand excluded by PLIP TL.59: 3 residues within 4Å: Chain J: E.131, N.264, G.265 Ligand excluded by PLIP TL.64: 5 residues within 4Å: Chain J: D.50, S.53 Chain K: Y.179, E.212 Ligands: MN.61 Ligand excluded by PLIP TL.65: 3 residues within 4Å: Chain K: E.131, N.264, G.265 Ligand excluded by PLIP TL.70: 5 residues within 4Å: Chain K: D.50, S.53 Chain L: Y.179, E.212 Ligands: MN.67 Ligand excluded by PLIP TL.71: 3 residues within 4Å: Chain L: E.131, N.264, G.265 Ligand excluded by PLIP

12 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 8 residues within 4Å: Chain A: F.16, F.80, A.81, D.82, T.84 Chain F: Q.189, D.190, S.193 8 PLIP interactions: 4 interactions with chain F, 4 interactions with chain A Hydrophobic interactions: F:D.190, A:F.16 Hydrogen bonds: F:Q.189, F:D.190, A:A.81, A:D.82, A:D.82 Water bridges: F:E.194 MPD.12: 8 residues within 4Å: Chain A: Q.189, D.190, S.193 Chain B: F.16, F.80, A.81, D.82, T.84 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:D.190, B:F.16 Hydrogen bonds: A:Q.189, A:D.190, B:A.81, B:D.82, B:D.82 Water bridges: A:E.194 MPD.18: 8 residues within 4Å: Chain B: Q.189, D.190, S.193 Chain C: F.16, F.80, A.81, D.82, T.84 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:D.190, C:F.16 Hydrogen bonds: B:Q.189, B:D.190, C:A.81, C:D.82, C:D.82 Water bridges: B:E.194 MPD.24: 8 residues within 4Å: Chain C: Q.189, D.190, S.193 Chain D: F.16, F.80, A.81, D.82, T.84 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:F.16, C:D.190 Hydrogen bonds: D:A.81, D:D.82, D:D.82, C:Q.189, C:D.190 Water bridges: C:E.194 MPD.30: 8 residues within 4Å: Chain D: Q.189, D.190, S.193 Chain E: F.16, F.80, A.81, D.82, T.84 8 PLIP interactions: 4 interactions with chain E, 4 interactions with chain D Hydrophobic interactions: E:F.16, D:D.190 Hydrogen bonds: E:A.81, E:D.82, E:D.82, D:Q.189, D:D.190 Water bridges: D:E.194 MPD.36: 8 residues within 4Å: Chain E: Q.189, D.190, S.193 Chain F: F.16, F.80, A.81, D.82, T.84 8 PLIP interactions: 4 interactions with chain E, 4 interactions with chain F Hydrophobic interactions: E:D.190, F:F.16 Hydrogen bonds: E:Q.189, E:D.190, F:A.81, F:D.82, F:D.82 Water bridges: E:E.194 MPD.42: 8 residues within 4Å: Chain G: F.16, F.80, A.81, D.82, T.84 Chain H: Q.189, D.190, S.193 8 PLIP interactions: 4 interactions with chain G, 4 interactions with chain H Hydrophobic interactions: G:F.16 Hydrogen bonds: G:A.81, G:D.82, G:T.84, H:Q.189, H:D.190, H:D.190 Water bridges: H:E.194 MPD.48: 8 residues within 4Å: Chain H: F.16, F.80, A.81, D.82, T.84 Chain I: Q.189, D.190, S.193 10 PLIP interactions: 4 interactions with chain H, 6 interactions with chain I Hydrophobic interactions: H:F.16, I:D.190 Hydrogen bonds: H:A.81, H:D.82, H:T.84, I:Q.189, I:D.190, I:D.190, I:S.193 Water bridges: I:E.194 MPD.54: 8 residues within 4Å: Chain I: F.16, F.80, A.81, D.82, T.84 Chain J: Q.189, D.190, S.193 10 PLIP interactions: 4 interactions with chain I, 6 interactions with chain J Hydrophobic interactions: I:F.16, J:D.190 Hydrogen bonds: I:A.81, I:D.82, I:T.84, J:Q.189, J:D.190, J:D.190, J:S.193 Water bridges: J:E.194 MPD.60: 8 residues within 4Å: Chain J: F.16, F.80, A.81, D.82, T.84 Chain K: Q.189, D.190, S.193 10 PLIP interactions: 4 interactions with chain J, 6 interactions with chain K Hydrophobic interactions: J:F.16, K:D.190 Hydrogen bonds: J:A.81, J:D.82, J:T.84, K:Q.189, K:D.190, K:D.190, K:S.193 Water bridges: K:E.194 MPD.66: 8 residues within 4Å: Chain K: F.16, F.80, A.81, D.82, T.84 Chain L: Q.189, D.190, S.193 9 PLIP interactions: 5 interactions with chain L, 4 interactions with chain K Hydrophobic interactions: L:D.190, K:F.16 Hydrogen bonds: L:Q.189, L:D.190, L:D.190, K:A.81, K:D.82, K:T.84 Water bridges: L:E.194 MPD.72: 8 residues within 4Å: Chain G: Q.189, D.190, S.193 Chain L: F.16, F.80, A.81, D.82, T.84 10 PLIP interactions: 6 interactions with chain G, 4 interactions with chain L Hydrophobic interactions: G:D.190, L:F.16 Hydrogen bonds: G:Q.189, G:D.190, G:D.190, G:S.193, L:A.81, L:D.82, L:T.84 Water bridges: G:E.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gill, H.S. et al., The crystal structure of phosphinothricin in the active site of glutamine synthetase illuminates the mechanism of enzymatic inhibition. Biochemistry (2001)

Release Date

2001-04-04

Peptides

PROTEIN (GLUTAMINE SYNTHETASE): ABCDEFGHIJKL

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

K
K

L
L

PROTEIN (GLUTAMINE SYNTHETASE)

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