SMTL ID : 1f52.1

CRYSTAL STRUCTURE OF GLUTAMINE SYNTHETASE FROM SALMONELLA TYPHIMURIUM CO-CRYSTALLIZED WITH ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

homo-12-mer

Ligands

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

MN.1: 3 residues within 4Å: Chain A: E.131, E.212, E.220 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.131, A:E.212, A:E.220, H2O.10, H2O.10 MN.2: 6 residues within 4Å: Chain A: E.129, H.269, H.271, E.357, R.359 Ligands: ADP.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.129, A:H.269, A:E.357, H2O.10, H2O.10 MN.6: 3 residues within 4Å: Chain B: E.131, E.212, E.220 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.131, B:E.212, B:E.220, H2O.22, H2O.22 MN.7: 6 residues within 4Å: Chain B: E.129, H.269, H.271, E.357, R.359 Ligands: ADP.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.129, B:H.269, B:E.357, H2O.22, H2O.22 MN.11: 3 residues within 4Å: Chain C: E.131, E.212, E.220 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.131, C:E.212, C:E.220, H2O.33, H2O.33 MN.12: 6 residues within 4Å: Chain C: E.129, H.269, H.271, E.357, R.359 Ligands: ADP.13 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.129, C:H.269, C:E.357, H2O.33, H2O.33 MN.16: 3 residues within 4Å: Chain D: E.131, E.212, E.220 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.131, D:E.212, D:E.220, H2O.44, H2O.44 MN.17: 6 residues within 4Å: Chain D: E.129, H.269, H.271, E.357, R.359 Ligands: ADP.18 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.129, D:H.269, D:E.357, H2O.44, H2O.45 MN.21: 3 residues within 4Å: Chain E: E.131, E.212, E.220 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.131, E:E.212, E:E.220, H2O.56, H2O.56 MN.22: 6 residues within 4Å: Chain E: E.129, H.269, H.271, E.357, R.359 Ligands: ADP.23 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.129, E:H.269, E:E.357, H2O.56, H2O.56 MN.26: 3 residues within 4Å: Chain F: E.131, E.212, E.220 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.131, F:E.212, F:E.220, H2O.67, H2O.67 MN.27: 6 residues within 4Å: Chain F: E.129, H.269, H.271, E.357, R.359 Ligands: ADP.28 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.129, F:H.269, F:E.357, H2O.67, H2O.68 MN.31: 3 residues within 4Å: Chain G: E.131, E.212, E.220 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.131, G:E.212, G:E.220, H2O.78, H2O.78 MN.32: 6 residues within 4Å: Chain G: E.129, H.269, H.271, E.357, R.359 Ligands: ADP.33 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.129, G:H.269, G:E.357, H2O.78, H2O.79 MN.36: 3 residues within 4Å: Chain H: E.131, E.212, E.220 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.131, H:E.212, H:E.220, H2O.90, H2O.90 MN.37: 6 residues within 4Å: Chain H: E.129, H.269, H.271, E.357, R.359 Ligands: ADP.38 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.129, H:H.269, H:E.357, H2O.90, H2O.90 MN.41: 3 residues within 4Å: Chain I: E.131, E.212, E.220 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:E.131, I:E.212, I:E.220, H2O.101, H2O.101 MN.42: 6 residues within 4Å: Chain I: E.129, H.269, H.271, E.357, R.359 Ligands: ADP.43 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:E.129, I:H.269, I:E.357, H2O.101, H2O.101 MN.46: 3 residues within 4Å: Chain J: E.131, E.212, E.220 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.131, J:E.212, J:E.220, H2O.112, H2O.112 MN.47: 6 residues within 4Å: Chain J: E.129, H.269, H.271, E.357, R.359 Ligands: ADP.48 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.129, J:H.269, J:E.357, H2O.112, H2O.112 MN.51: 3 residues within 4Å: Chain K: E.131, E.212, E.220 5 PLIP interactions: 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:E.131, K:E.212, K:E.220, H2O.123, H2O.123 MN.52: 6 residues within 4Å: Chain K: E.129, H.269, H.271, E.357, R.359 Ligands: ADP.53 5 PLIP interactions: 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:E.129, K:H.269, K:E.357, H2O.123, H2O.123 MN.56: 3 residues within 4Å: Chain L: E.131, E.212, E.220 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:E.131, L:E.212, L:E.220, H2O.134, H2O.135 MN.57: 6 residues within 4Å: Chain L: E.129, H.269, H.271, E.357, R.359 Ligands: ADP.58 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:E.129, L:H.269, L:E.357, H2O.135, H2O.135

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

ADP.3: 15 residues within 4Å: Chain A: L.125, G.127, E.129, E.207, A.222, T.223, R.224, F.225, H.271, S.273, R.344, A.353, R.355, E.357 Ligands: MN.2 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.207, A:F.225, A:S.273, A:S.273 Water bridges: A:E.220, A:R.339, A:R.339, A:R.344, B:D.50 Salt bridges: A:H.271, A:R.344 ADP.8: 15 residues within 4Å: Chain B: L.125, G.127, E.129, E.207, A.222, T.223, R.224, F.225, H.271, S.273, R.344, A.353, R.355, E.357 Ligands: MN.7 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:E.207, B:F.225, B:S.273, B:S.273 Water bridges: B:E.220, B:R.339, B:R.339, B:R.344, C:D.50 Salt bridges: B:H.271, B:R.344 ADP.13: 15 residues within 4Å: Chain C: L.125, G.127, E.129, E.207, A.222, T.223, R.224, F.225, H.271, S.273, R.344, A.353, R.355, E.357 Ligands: MN.12 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.207, C:F.225, C:S.273, C:S.273 Water bridges: C:E.220, C:R.339, C:R.339, C:R.344, D:D.50 Salt bridges: C:H.271, C:R.344 ADP.18: 15 residues within 4Å: Chain D: L.125, G.127, E.129, E.207, A.222, T.223, R.224, F.225, H.271, S.273, R.344, A.353, R.355, E.357 Ligands: MN.17 11 PLIP interactions: 1 interactions with chain E, 10 interactions with chain D Water bridges: E:D.50, D:E.220, D:R.339, D:R.339, D:R.344 Hydrogen bonds: D:E.207, D:F.225, D:S.273, D:S.273 Salt bridges: D:H.271, D:R.344 ADP.23: 15 residues within 4Å: Chain E: L.125, G.127, E.129, E.207, A.222, T.223, R.224, F.225, H.271, S.273, R.344, A.353, R.355, E.357 Ligands: MN.22 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:E.207, E:F.225, E:S.273, E:S.273 Water bridges: E:E.220, E:R.339, E:R.339, E:R.344, F:D.50 Salt bridges: E:H.271, E:R.344 ADP.28: 15 residues within 4Å: Chain F: L.125, G.127, E.129, E.207, A.222, T.223, R.224, F.225, H.271, S.273, R.344, A.353, R.355, E.357 Ligands: MN.27 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:E.207, F:F.225, F:S.273, F:S.273 Water bridges: F:E.220, F:R.339, F:R.339, F:R.344, A:D.50 Salt bridges: F:H.271, F:R.344 ADP.33: 15 residues within 4Å: Chain G: L.125, G.127, E.129, E.207, A.222, T.223, R.224, F.225, H.271, S.273, R.344, A.353, R.355, E.357 Ligands: MN.32 11 PLIP interactions: 10 interactions with chain G, 1 interactions with chain L Hydrogen bonds: G:E.207, G:F.225, G:S.273, G:S.273 Water bridges: G:E.220, G:R.339, G:R.339, G:R.344, L:D.50 Salt bridges: G:H.271, G:R.344 ADP.38: 15 residues within 4Å: Chain H: L.125, G.127, E.129, E.207, A.222, T.223, R.224, F.225, H.271, S.273, R.344, A.353, R.355, E.357 Ligands: MN.37 11 PLIP interactions: 10 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:E.207, H:F.225, H:S.273, H:S.273 Water bridges: H:E.220, H:R.339, H:R.339, H:R.344, G:D.50 Salt bridges: H:H.271, H:R.344 ADP.43: 15 residues within 4Å: Chain I: L.125, G.127, E.129, E.207, A.222, T.223, R.224, F.225, H.271, S.273, R.344, A.353, R.355, E.357 Ligands: MN.42 11 PLIP interactions: 10 interactions with chain I, 1 interactions with chain H Hydrogen bonds: I:E.207, I:F.225, I:S.273, I:S.273 Water bridges: I:E.220, I:R.339, I:R.339, I:R.344, H:D.50 Salt bridges: I:H.271, I:R.344 ADP.48: 15 residues within 4Å: Chain J: L.125, G.127, E.129, E.207, A.222, T.223, R.224, F.225, H.271, S.273, R.344, A.353, R.355, E.357 Ligands: MN.47 11 PLIP interactions: 10 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:E.207, J:F.225, J:S.273, J:S.273 Water bridges: J:E.220, J:R.339, J:R.339, J:R.344, I:D.50 Salt bridges: J:H.271, J:R.344 ADP.53: 15 residues within 4Å: Chain K: L.125, G.127, E.129, E.207, A.222, T.223, R.224, F.225, H.271, S.273, R.344, A.353, R.355, E.357 Ligands: MN.52 11 PLIP interactions: 10 interactions with chain K, 1 interactions with chain J Hydrogen bonds: K:E.207, K:F.225, K:S.273, K:S.273 Water bridges: K:E.220, K:R.339, K:R.339, K:R.344, J:D.50 Salt bridges: K:H.271, K:R.344 ADP.58: 15 residues within 4Å: Chain L: L.125, G.127, E.129, E.207, A.222, T.223, R.224, F.225, H.271, S.273, R.344, A.353, R.355, E.357 Ligands: MN.57 11 PLIP interactions: 10 interactions with chain L, 1 interactions with chain K Hydrogen bonds: L:E.207, L:F.225, L:S.273, L:S.273 Water bridges: L:E.220, L:R.339, L:R.339, L:R.344, K:D.50 Salt bridges: L:H.271, L:R.344

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

MPD.4: 10 residues within 4Å: Chain A: R.20, F.21, T.22, R.88, C.89, D.90, D.103, R.105, D.233, Y.368 Ligand excluded by PLIP MPD.5: 9 residues within 4Å: Chain A: F.16, F.80, A.81, D.82, T.84 Chain F: Q.189, D.190, S.193, H.209 Ligand excluded by PLIP MPD.9: 9 residues within 4Å: Chain A: Q.189, D.190, S.193, H.209 Chain B: F.16, F.80, A.81, D.82, T.84 Ligand excluded by PLIP MPD.10: 10 residues within 4Å: Chain B: R.20, F.21, T.22, R.88, C.89, D.90, D.103, R.105, D.233, Y.368 Ligand excluded by PLIP MPD.14: 9 residues within 4Å: Chain B: Q.189, D.190, S.193, H.209 Chain C: F.16, F.80, A.81, D.82, T.84 Ligand excluded by PLIP MPD.15: 10 residues within 4Å: Chain C: R.20, F.21, T.22, R.88, C.89, D.90, D.103, R.105, D.233, Y.368 Ligand excluded by PLIP MPD.19: 9 residues within 4Å: Chain C: Q.189, D.190, S.193, H.209 Chain D: F.16, F.80, A.81, D.82, T.84 Ligand excluded by PLIP MPD.20: 10 residues within 4Å: Chain D: R.20, F.21, T.22, R.88, C.89, D.90, D.103, R.105, D.233, Y.368 Ligand excluded by PLIP MPD.24: 9 residues within 4Å: Chain D: Q.189, D.190, S.193, H.209 Chain E: F.16, F.80, A.81, D.82, T.84 Ligand excluded by PLIP MPD.25: 10 residues within 4Å: Chain E: R.20, F.21, T.22, R.88, C.89, D.90, D.103, R.105, D.233, Y.368 Ligand excluded by PLIP MPD.29: 9 residues within 4Å: Chain E: Q.189, D.190, S.193, H.209 Chain F: F.16, F.80, A.81, D.82, T.84 Ligand excluded by PLIP MPD.30: 10 residues within 4Å: Chain F: R.20, F.21, T.22, R.88, C.89, D.90, D.103, R.105, D.233, Y.368 Ligand excluded by PLIP MPD.34: 10 residues within 4Å: Chain G: R.20, F.21, T.22, R.88, C.89, D.90, D.103, R.105, D.233, Y.368 Ligand excluded by PLIP MPD.35: 9 residues within 4Å: Chain G: F.16, F.80, A.81, D.82, T.84 Chain H: Q.189, D.190, S.193, H.209 Ligand excluded by PLIP MPD.39: 10 residues within 4Å: Chain H: R.20, F.21, T.22, R.88, C.89, D.90, D.103, R.105, D.233, Y.368 Ligand excluded by PLIP MPD.40: 9 residues within 4Å: Chain H: F.16, F.80, A.81, D.82, T.84 Chain I: Q.189, D.190, S.193, H.209 Ligand excluded by PLIP MPD.44: 10 residues within 4Å: Chain I: R.20, F.21, T.22, R.88, C.89, D.90, D.103, R.105, D.233, Y.368 Ligand excluded by PLIP MPD.45: 9 residues within 4Å: Chain I: F.16, F.80, A.81, D.82, T.84 Chain J: Q.189, D.190, S.193, H.209 Ligand excluded by PLIP MPD.49: 10 residues within 4Å: Chain J: R.20, F.21, T.22, R.88, C.89, D.90, D.103, R.105, D.233, Y.368 Ligand excluded by PLIP MPD.50: 9 residues within 4Å: Chain J: F.16, F.80, A.81, D.82, T.84 Chain K: Q.189, D.190, S.193, H.209 Ligand excluded by PLIP MPD.54: 10 residues within 4Å: Chain K: R.20, F.21, T.22, R.88, C.89, D.90, D.103, R.105, D.233, Y.368 Ligand excluded by PLIP MPD.55: 9 residues within 4Å: Chain K: F.16, F.80, A.81, D.82, T.84 Chain L: Q.189, D.190, S.193, H.209 Ligand excluded by PLIP MPD.59: 9 residues within 4Å: Chain G: Q.189, D.190, S.193, H.209 Chain L: F.16, F.80, A.81, D.82, T.84 Ligand excluded by PLIP MPD.60: 10 residues within 4Å: Chain L: R.20, F.21, T.22, R.88, C.89, D.90, D.103, R.105, D.233, Y.368 Ligand excluded by PLIP

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

2000-06-28

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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