SMTL ID : 5zlp.1

Crystal structure of glutamine synthetase from helicobacter pylori

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.93 Å

Oligo State

homo-12-mer

Ligands

6 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 18 residues within 4Å: Chain A: G.137, E.139, Y.190, F.218, V.219, H.221, E.230, V.233, K.234, F.235, H.281, S.283, R.349, N.362, S.363, R.365 Chain F: Y.43, P.58 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:G.137, A:E.139, A:Y.190, A:Y.190, A:E.230, A:V.233, A:F.235, A:S.283, A:S.283, A:R.365, F:Y.43 Water bridges: A:R.365 Salt bridges: A:H.221, A:H.281, A:R.349, A:R.365 pi-Stacking: A:F.235, A:F.235 pi-Cation interactions: A:R.365 ATP.2: 17 residues within 4Å: Chain B: G.137, A.138, E.139, F.218, V.233, K.234, F.235, H.279, H.281, S.283, R.349, R.354, N.362, S.363, A.364, R.365, E.367 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:G.137, B:E.139, B:V.233, B:F.235, B:H.279, B:S.283, B:S.283, B:E.367 Salt bridges: B:H.281, B:R.349, B:R.354, B:R.354, B:R.365, B:R.365 pi-Stacking: B:F.235 ATP.3: 18 residues within 4Å: Chain C: Y.135, G.137, A.138, E.139, F.218, E.230, V.233, K.234, F.235, H.279, H.281, S.283, R.349, R.354, N.362, S.363, R.365, E.367 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:V.233, C:F.235, C:S.283, C:N.362, C:R.365 Salt bridges: C:H.279, C:H.281, C:R.349, C:R.354, C:R.354, C:R.365 pi-Stacking: C:F.235, C:F.235 pi-Cation interactions: C:R.365 ATP.6: 15 residues within 4Å: Chain E: F.59 Chain F: G.137, E.139, Y.190, F.218, V.233, F.235, H.281, S.283, R.349, R.354, N.362, S.363, R.365, E.367 18 PLIP interactions: 16 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:E.139, F:Y.190, F:V.233, F:F.235, F:S.283, F:S.283, E:P.58, E:F.59 Salt bridges: F:H.281, F:H.281, F:R.349, F:R.349, F:R.354, F:R.365, F:R.365 pi-Stacking: F:F.235, F:F.235 pi-Cation interactions: F:R.365 ATP.11: 21 residues within 4Å: Chain H: P.58 Chain I: Y.135, G.137, A.138, E.139, F.218, V.219, V.233, K.234, F.235, H.279, H.281, S.283, R.349, R.354, P.356, N.362, S.363, A.364, R.365 Ligands: PPQ.12 15 PLIP interactions: 15 interactions with chain I Hydrogen bonds: I:A.138, I:F.235, I:S.283, I:W.285, I:N.290, I:R.365 Water bridges: I:E.139, I:H.221, I:R.349, I:R.349 Salt bridges: I:H.281, I:H.281, I:R.349, I:R.354 pi-Cation interactions: I:R.365 ATP.17: 17 residues within 4Å: Chain K: Y.135, G.137, A.138, E.139, F.218, V.233, K.234, F.235, H.281, S.283, W.285, R.349, R.354, P.356, N.362, R.365, E.367 18 PLIP interactions: 18 interactions with chain K Hydrogen bonds: K:G.137, K:A.138, K:V.233, K:F.235, K:H.279, K:S.283, K:N.362, K:R.365 Water bridges: K:R.369 Salt bridges: K:H.281, K:H.281, K:R.349, K:R.354, K:R.354, K:R.365 pi-Stacking: K:F.235, K:F.235 pi-Cation interactions: K:R.365

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

ADP.4: 15 residues within 4Å: Chain D: Y.135, G.137, E.139, F.218, V.233, K.234, F.235, H.281, S.283, W.285, R.354, N.362, S.363, R.365, E.367 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:V.233, D:F.235, D:S.283, D:S.283, D:R.349, D:R.365 Salt bridges: D:H.281, D:R.354 pi-Stacking: D:F.235 pi-Cation interactions: D:R.365 ADP.5: 14 residues within 4Å: Chain E: Y.135, G.137, E.139, F.218, V.233, K.234, F.235, H.281, S.283, R.354, N.362, S.363, R.365, E.367 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:A.138, E:F.235, E:S.283, E:S.283, E:R.365, E:E.367 Water bridges: E:R.365, E:R.365 Salt bridges: E:H.281, E:R.354, E:R.365, E:R.365 pi-Stacking: E:F.235, E:F.235 ADP.7: 18 residues within 4Å: Chain G: Y.135, G.137, E.139, F.218, E.230, V.233, K.234, F.235, H.281, S.283, W.285, N.290, R.349, R.354, N.362, A.364, R.365, E.367 13 PLIP interactions: 13 interactions with chain G Hydrogen bonds: G:A.138, G:F.235, G:S.283, G:W.285, G:N.290, G:R.365 Salt bridges: G:H.281, G:H.281, G:R.349, G:R.354 pi-Stacking: G:F.235, G:F.235 pi-Cation interactions: G:R.365 ADP.8: 15 residues within 4Å: Chain H: Y.135, G.137, E.139, F.218, V.233, F.235, H.281, V.282, S.283, W.285, N.290, R.354, P.356, N.362, R.365 13 PLIP interactions: 13 interactions with chain H Hydrogen bonds: H:F.235, H:S.283, H:W.285, H:N.290 Water bridges: H:A.138, H:V.233 Salt bridges: H:H.281, H:H.281, H:R.354, H:R.365 pi-Stacking: H:F.235, H:F.235 pi-Cation interactions: H:R.365 ADP.15: 19 residues within 4Å: Chain J: Y.135, G.137, A.138, E.139, F.218, V.233, K.234, F.235, H.281, S.283, W.285, N.290, R.349, R.354, N.362, R.365, E.367 Ligands: P3P.13, MG.16 13 PLIP interactions: 13 interactions with chain J Hydrogen bonds: J:F.235, J:S.283, J:W.285, J:N.290, J:R.349, J:R.365 Water bridges: J:A.138, J:V.233, J:R.365 Salt bridges: J:H.281, J:H.281, J:R.354, J:R.365 ADP.18: 13 residues within 4Å: Chain L: G.137, A.138, E.139, F.218, V.233, K.234, F.235, H.281, S.283, N.290, R.354, N.362, R.365 14 PLIP interactions: 14 interactions with chain L Hydrogen bonds: L:G.137, L:A.138, L:V.233, L:F.235, L:S.283, L:N.290, L:R.349, L:N.362 Water bridges: L:A.138, L:V.233 Salt bridges: L:H.281, L:R.354, L:R.365 pi-Cation interactions: L:R.365

3 x PPQ: PHOSPHINOTHRICIN(Non-covalent)

PPQ.9: 14 residues within 4Å: Chain H: E.141, E.223, N.274, G.275, G.277, H.279, R.331, Y.336, E.337, A.338, R.349, R.369 Chain L: D.60 Ligands: MG.10 9 PLIP interactions: 8 interactions with chain H, 1 interactions with chain L Hydrogen bonds: H:E.141, H:E.223, H:N.274, H:Y.336, H:E.337, H:R.369, L:D.60 Salt bridges: H:H.279, H:R.331 PPQ.12: 14 residues within 4Å: Chain H: D.60 Chain I: E.141, E.223, N.274, G.275, G.277, H.279, R.331, Y.336, E.337, A.338, R.349, R.369 Ligands: ATP.11 11 PLIP interactions: 1 interactions with chain H, 10 interactions with chain I Hydrogen bonds: H:D.60, I:E.141, I:N.274, I:G.275, I:G.277, I:E.337, I:R.369 Hydrophobic interactions: I:E.337 Salt bridges: I:H.279, I:R.331, I:R.369 PPQ.19: 14 residues within 4Å: Chain G: D.60 Chain L: E.141, Y.190, E.223, E.230, N.274, G.275, H.279, R.331, Y.336, E.337, R.349, R.369 Ligands: MG.20 10 PLIP interactions: 9 interactions with chain L, 1 interactions with chain G Hydrogen bonds: L:E.141, L:G.275, L:Y.336, L:R.349, L:R.349, L:R.369, G:D.60 Salt bridges: L:H.279, L:R.331, L:R.369

4 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 5 residues within 4Å: Chain H: E.139, E.141, E.223, E.230 Ligands: PPQ.9 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.141, H:E.223, H:E.230 MG.14: 6 residues within 4Å: Chain J: E.139, E.141, E.223, E.230, H.279 Ligands: P3P.13 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.141, J:E.223, J:E.230 MG.16: 4 residues within 4Å: Chain J: H.221, E.230 Ligands: P3P.13, ADP.15 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:E.230 MG.20: 5 residues within 4Å: Chain L: E.139, E.141, E.223, E.230 Ligands: PPQ.19 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.141, L:E.223, L:E.230

1 x P3P: (2S)-2-AMINO-4-[METHYL(PHOSPHONOOXY)PHOSPHORYL]BUTANOIC ACID(Non-covalent)

P3P.13: 20 residues within 4Å: Chain I: D.60 Chain J: E.139, E.141, E.223, Q.228, E.230, N.274, G.275, S.276, G.277, H.279, R.331, Y.336, E.337, R.349, E.367, R.369 Ligands: MG.14, ADP.15, MG.16 13 PLIP interactions: 13 interactions with chain J Hydrophobic interactions: J:E.337 Hydrogen bonds: J:E.139, J:Q.228, J:N.274, J:G.275, J:G.275, J:R.369, J:R.369 Salt bridges: J:H.279, J:H.279, J:R.331, J:R.349, J:R.369

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joo, H.K. et al., Structural Analysis of Glutamine Synthetase from Helicobacter pylori. Sci Rep (2018)

Release Date

2018-08-29

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
H

H
J

I
K

J
L

K
G

L
I

Glutamine synthetase

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