SMTL ID : 1fpy.1

CRYSTAL STRUCTURE OF GLUTAMINE SYNTHETASE FROM SALMONELLA TYPHIMURIUM WITH INHIBITOR PHOSPHINOTHRICIN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

homo-12-mer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: E.131, E.212, E.220 Ligands: PPQ.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.131, A:E.212, A:E.220 MN.2: 6 residues within 4Å: Chain A: E.129, H.269, E.357, R.359 Ligands: ADP.3, PPQ.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.129, A:H.269, A:E.357 MN.5: 4 residues within 4Å: Chain B: E.131, E.212, E.220 Ligands: PPQ.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.131, B:E.212, B:E.220 MN.6: 6 residues within 4Å: Chain B: E.129, H.269, E.357, R.359 Ligands: ADP.7, PPQ.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.129, B:H.269, B:E.357 MN.9: 4 residues within 4Å: Chain C: E.131, E.212, E.220 Ligands: PPQ.12 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.131, C:E.212, C:E.220 MN.10: 6 residues within 4Å: Chain C: E.129, H.269, E.357, R.359 Ligands: ADP.11, PPQ.12 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.129, C:H.269, C:E.357 MN.13: 4 residues within 4Å: Chain D: E.131, E.212, E.220 Ligands: PPQ.16 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.131, D:E.212, D:E.220 MN.14: 6 residues within 4Å: Chain D: E.129, H.269, E.357, R.359 Ligands: ADP.15, PPQ.16 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.129, D:H.269, D:E.357 MN.17: 4 residues within 4Å: Chain E: E.131, E.212, E.220 Ligands: PPQ.20 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.131, E:E.212, E:E.220 MN.18: 6 residues within 4Å: Chain E: E.129, H.269, E.357, R.359 Ligands: ADP.19, PPQ.20 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.129, E:H.269, E:E.357 MN.21: 4 residues within 4Å: Chain F: E.131, E.212, E.220 Ligands: PPQ.24 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.131, F:E.212, F:E.220 MN.22: 6 residues within 4Å: Chain F: E.129, H.269, E.357, R.359 Ligands: ADP.23, PPQ.24 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.129, F:H.269, F:E.357 MN.25: 4 residues within 4Å: Chain G: E.131, E.212, E.220 Ligands: PPQ.28 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.131, G:E.212, G:E.220 MN.26: 6 residues within 4Å: Chain G: E.129, H.269, E.357, R.359 Ligands: ADP.27, PPQ.28 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.129, G:H.269, G:E.357 MN.29: 4 residues within 4Å: Chain H: E.131, E.212, E.220 Ligands: PPQ.32 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.131, H:E.212, H:E.220 MN.30: 6 residues within 4Å: Chain H: E.129, H.269, E.357, R.359 Ligands: ADP.31, PPQ.32 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.129, H:H.269, H:E.357 MN.33: 4 residues within 4Å: Chain I: E.131, E.212, E.220 Ligands: PPQ.36 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:E.131, I:E.212, I:E.220 MN.34: 6 residues within 4Å: Chain I: E.129, H.269, E.357, R.359 Ligands: ADP.35, PPQ.36 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:E.129, I:H.269, I:E.357 MN.37: 4 residues within 4Å: Chain J: E.131, E.212, E.220 Ligands: PPQ.40 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.131, J:E.212, J:E.220 MN.38: 6 residues within 4Å: Chain J: E.129, H.269, E.357, R.359 Ligands: ADP.39, PPQ.40 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.129, J:H.269, J:E.357 MN.41: 4 residues within 4Å: Chain K: E.131, E.212, E.220 Ligands: PPQ.44 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:E.131, K:E.212, K:E.220 MN.42: 6 residues within 4Å: Chain K: E.129, H.269, E.357, R.359 Ligands: ADP.43, PPQ.44 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:E.129, K:H.269, K:E.357 MN.45: 4 residues within 4Å: Chain L: E.131, E.212, E.220 Ligands: PPQ.48 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.131, L:E.212, L:E.220 MN.46: 6 residues within 4Å: Chain L: E.129, H.269, E.357, R.359 Ligands: ADP.47, PPQ.48 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.129, L:H.269, L:E.357

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

ADP.3: 14 residues within 4Å: Chain A: G.127, E.129, E.207, E.220, A.222, T.223, R.224, F.225, H.271, S.273, A.353, R.355, E.357 Ligands: MN.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:E.207, A:E.220, A:F.225, A:S.273, A:S.273, A:R.344, A:R.355 Water bridges: A:E.207 Salt bridges: A:H.271, A:H.271 pi-Stacking: A:F.225, A:F.225 ADP.7: 14 residues within 4Å: Chain B: G.127, E.129, E.207, E.220, A.222, T.223, R.224, F.225, H.271, S.273, A.353, R.355, E.357 Ligands: MN.6 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:E.207, B:E.220, B:F.225, B:S.273, B:S.273, B:R.344, B:R.355 Water bridges: B:E.207 Salt bridges: B:H.271, B:H.271 pi-Stacking: B:F.225, B:F.225 ADP.11: 14 residues within 4Å: Chain C: G.127, E.129, E.207, E.220, A.222, T.223, R.224, F.225, H.271, S.273, A.353, R.355, E.357 Ligands: MN.10 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:E.207, C:E.220, C:F.225, C:S.273, C:S.273, C:R.344, C:R.355 Water bridges: C:E.207 Salt bridges: C:H.271, C:H.271 pi-Stacking: C:F.225, C:F.225 ADP.15: 14 residues within 4Å: Chain D: G.127, E.129, E.207, E.220, A.222, T.223, R.224, F.225, H.271, S.273, A.353, R.355, E.357 Ligands: MN.14 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:E.207, D:E.220, D:F.225, D:S.273, D:S.273, D:R.344, D:R.355 Water bridges: D:E.207 Salt bridges: D:H.271, D:H.271 pi-Stacking: D:F.225, D:F.225 ADP.19: 14 residues within 4Å: Chain E: G.127, E.129, E.207, E.220, A.222, T.223, R.224, F.225, H.271, S.273, A.353, R.355, E.357 Ligands: MN.18 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:E.207, E:E.220, E:F.225, E:S.273, E:S.273, E:R.344, E:R.355 Water bridges: E:E.207 Salt bridges: E:H.271, E:H.271 pi-Stacking: E:F.225, E:F.225 ADP.23: 14 residues within 4Å: Chain F: G.127, E.129, E.207, E.220, A.222, T.223, R.224, F.225, H.271, S.273, A.353, R.355, E.357 Ligands: MN.22 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:E.207, F:E.220, F:F.225, F:S.273, F:S.273, F:R.344, F:R.355 Water bridges: F:E.207 Salt bridges: F:H.271, F:H.271 pi-Stacking: F:F.225, F:F.225 ADP.27: 14 residues within 4Å: Chain G: G.127, E.129, E.207, E.220, A.222, T.223, R.224, F.225, H.271, S.273, A.353, R.355, E.357 Ligands: MN.26 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:E.207, G:E.220, G:F.225, G:H.271, G:S.273, G:S.273, G:R.344, G:R.355 Salt bridges: G:H.271, G:H.271 pi-Stacking: G:F.225, G:F.225 ADP.31: 14 residues within 4Å: Chain H: G.127, E.129, E.207, E.220, A.222, T.223, R.224, F.225, H.271, S.273, A.353, R.355, E.357 Ligands: MN.30 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:E.129, H:E.207, H:E.220, H:F.225, H:H.271, H:S.273, H:S.273, H:R.344, H:R.355, H:E.357 Salt bridges: H:H.271, H:H.271 pi-Stacking: H:F.225, H:F.225 ADP.35: 14 residues within 4Å: Chain I: G.127, E.129, E.207, E.220, A.222, T.223, R.224, F.225, H.271, S.273, A.353, R.355, E.357 Ligands: MN.34 12 PLIP interactions: 12 interactions with chain I Hydrogen bonds: I:E.207, I:E.220, I:F.225, I:H.271, I:S.273, I:S.273, I:R.344, I:R.355 Salt bridges: I:H.271, I:H.271 pi-Stacking: I:F.225, I:F.225 ADP.39: 14 residues within 4Å: Chain J: G.127, E.129, E.207, E.220, A.222, T.223, R.224, F.225, H.271, S.273, A.353, R.355, E.357 Ligands: MN.38 12 PLIP interactions: 12 interactions with chain J Hydrogen bonds: J:E.207, J:E.220, J:F.225, J:H.271, J:S.273, J:S.273, J:R.344, J:R.355 Salt bridges: J:H.271, J:H.271 pi-Stacking: J:F.225, J:F.225 ADP.43: 14 residues within 4Å: Chain K: G.127, E.129, E.207, E.220, A.222, T.223, R.224, F.225, H.271, S.273, A.353, R.355, E.357 Ligands: MN.42 12 PLIP interactions: 12 interactions with chain K Hydrogen bonds: K:E.207, K:E.220, K:F.225, K:H.271, K:S.273, K:S.273, K:R.344, K:R.355 Salt bridges: K:H.271, K:H.271 pi-Stacking: K:F.225, K:F.225 ADP.47: 14 residues within 4Å: Chain L: G.127, E.129, E.207, E.220, A.222, T.223, R.224, F.225, H.271, S.273, A.353, R.355, E.357 Ligands: MN.46 12 PLIP interactions: 12 interactions with chain L Hydrogen bonds: L:E.207, L:E.220, L:F.225, L:H.271, L:S.273, L:S.273, L:R.344, L:R.355 Salt bridges: L:H.271, L:H.271 pi-Stacking: L:F.225, L:F.225

12 x PPQ: PHOSPHINOTHRICIN(Non-covalent)

PPQ.4: 11 residues within 4Å: Chain A: E.131, E.212, G.265, S.266, G.267, H.269, R.321, E.327, R.359 Ligands: MN.1, MN.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.131, A:G.265, A:G.267, A:E.327 Salt bridges: A:H.269, A:R.321 PPQ.8: 11 residues within 4Å: Chain B: E.131, E.212, G.265, S.266, G.267, H.269, R.321, E.327, R.359 Ligands: MN.5, MN.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.131, B:G.265, B:G.267, B:E.327 Salt bridges: B:H.269, B:R.321 PPQ.12: 11 residues within 4Å: Chain C: E.131, E.212, G.265, S.266, G.267, H.269, R.321, E.327, R.359 Ligands: MN.9, MN.10 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.131, C:G.265, C:G.267, C:E.327 Salt bridges: C:H.269, C:R.321 PPQ.16: 11 residues within 4Å: Chain D: E.131, E.212, G.265, S.266, G.267, H.269, R.321, E.327, R.359 Ligands: MN.13, MN.14 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:E.131, D:G.265, D:G.267, D:E.327 Salt bridges: D:H.269, D:R.321 PPQ.20: 11 residues within 4Å: Chain E: E.131, E.212, G.265, S.266, G.267, H.269, R.321, E.327, R.359 Ligands: MN.17, MN.18 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:E.131, E:G.265, E:G.267, E:E.327 Salt bridges: E:H.269, E:R.321 PPQ.24: 11 residues within 4Å: Chain F: E.131, E.212, G.265, S.266, G.267, H.269, R.321, E.327, R.359 Ligands: MN.21, MN.22 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:E.131, F:G.265, F:G.267, F:E.327 Salt bridges: F:H.269, F:R.321 PPQ.28: 11 residues within 4Å: Chain G: E.131, E.212, G.265, S.266, G.267, H.269, R.321, E.327, R.359 Ligands: MN.25, MN.26 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:E.131, G:G.265, G:G.267, G:E.327 Salt bridges: G:H.269, G:R.321 PPQ.32: 11 residues within 4Å: Chain H: E.131, E.212, G.265, S.266, G.267, H.269, R.321, E.327, R.359 Ligands: MN.29, MN.30 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:E.131, H:G.265, H:G.267, H:E.327 Salt bridges: H:H.269, H:R.321 PPQ.36: 11 residues within 4Å: Chain I: E.131, E.212, G.265, S.266, G.267, H.269, R.321, E.327, R.359 Ligands: MN.33, MN.34 6 PLIP interactions: 6 interactions with chain I Hydrogen bonds: I:E.131, I:G.265, I:G.267, I:E.327 Salt bridges: I:H.269, I:R.321 PPQ.40: 11 residues within 4Å: Chain J: E.131, E.212, G.265, S.266, G.267, H.269, R.321, E.327, R.359 Ligands: MN.37, MN.38 6 PLIP interactions: 6 interactions with chain J Hydrogen bonds: J:E.131, J:G.265, J:G.267, J:E.327 Salt bridges: J:H.269, J:R.321 PPQ.44: 11 residues within 4Å: Chain K: E.131, E.212, G.265, S.266, G.267, H.269, R.321, E.327, R.359 Ligands: MN.41, MN.42 6 PLIP interactions: 6 interactions with chain K Hydrogen bonds: K:E.131, K:G.265, K:G.267, K:E.327 Salt bridges: K:H.269, K:R.321 PPQ.48: 11 residues within 4Å: Chain L: E.131, E.212, G.265, S.266, G.267, H.269, R.321, E.327, R.359 Ligands: MN.45, MN.46 6 PLIP interactions: 6 interactions with chain L Hydrogen bonds: L:E.131, L:G.265, L:G.267, L:E.327 Salt bridges: L:H.269, L:R.321

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

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

GLUTAMINE SYNTHETASE

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