SMTL ID : 2d3b.1

Crystal Structure of the Maize Glutamine Synthetase complexed with AMPPNP and Methionine sulfoximine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-10-mer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: E.129, E.199, Q.201 Ligands: MN.3, ANP.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.129, A:E.199 MN.2: 6 residues within 4Å: Chain A: E.129, H.249, R.316, E.330, R.332 Ligands: ANP.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.129, A:E.129, A:H.249, A:E.330 MN.3: 7 residues within 4Å: Chain A: E.129, E.131, E.192, E.199 Ligands: MN.1, ANP.4, MSL.12 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.131, A:E.192, A:E.199 MN.5: 5 residues within 4Å: Chain B: E.129, E.199, Q.201 Ligands: MN.7, ANP.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.129, B:E.199 MN.6: 6 residues within 4Å: Chain B: E.129, H.249, R.316, E.330, R.332 Ligands: ANP.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.129, B:E.129, B:H.249, B:E.330 MN.7: 6 residues within 4Å: Chain B: E.131, E.192, E.199 Ligands: MN.5, ANP.8, MSL.13 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.131, B:E.192, B:E.199 MN.9: 5 residues within 4Å: Chain C: E.129, N.190, E.199 Ligands: MN.11, ANP.22 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.129, C:E.199 MN.10: 5 residues within 4Å: Chain C: E.129, H.249, E.330, R.332 Ligands: ANP.22 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.129, C:E.129, C:H.249, C:E.330 MN.11: 6 residues within 4Å: Chain C: E.131, E.192, E.199 Ligands: MN.9, MSL.14, ANP.22 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.131, C:E.192, C:E.199 MN.23: 4 residues within 4Å: Chain D: E.129, E.199 Ligands: MN.25, ANP.26 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.129, D:E.199 MN.24: 6 residues within 4Å: Chain D: E.129, H.249, R.316, E.330, R.332 Ligands: ANP.26 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.129, D:E.129, D:H.249, D:E.330 MN.25: 7 residues within 4Å: Chain D: E.129, E.131, E.192, E.199 Ligands: MSL.15, MN.23, ANP.26 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.131, D:E.192, D:E.199 MN.27: 5 residues within 4Å: Chain E: E.129, E.199 Ligands: MN.28, MN.29, ANP.30 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:E.129, E:E.199 MN.28: 7 residues within 4Å: Chain E: E.129, H.249, R.316, E.330, R.332 Ligands: MN.27, ANP.30 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:E.129, E:E.129, E:H.249, E:E.330 MN.29: 6 residues within 4Å: Chain E: E.131, E.192, E.199 Ligands: MSL.16, MN.27, ANP.30 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.131, E:E.192, E:E.199 MN.31: 4 residues within 4Å: Chain F: E.129, E.199 Ligands: MN.33, ANP.34 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:E.129, F:E.199 MN.32: 5 residues within 4Å: Chain F: E.129, H.249, E.330, R.332 Ligands: ANP.34 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:E.129, F:E.129, F:H.249, F:E.330 MN.33: 6 residues within 4Å: Chain F: E.131, E.192, E.199 Ligands: MSL.18, MN.31, ANP.34 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.131, F:E.192, F:E.199 MN.35: 4 residues within 4Å: Chain G: E.129, E.199 Ligands: MN.37, ANP.38 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:E.129, G:E.199 MN.36: 6 residues within 4Å: Chain G: E.129, H.249, R.316, E.330, R.332 Ligands: ANP.38 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:E.129, G:E.129, G:H.249, G:E.330 MN.37: 6 residues within 4Å: Chain G: E.131, E.192, E.199 Ligands: MSL.17, MN.35, ANP.38 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.131, G:E.192, G:E.199 MN.39: 5 residues within 4Å: Chain H: E.129, N.190, E.199, Q.201 Ligands: ANP.42 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:E.129, H:E.199 MN.40: 6 residues within 4Å: Chain H: E.129, H.249, R.316, E.330, R.332 Ligands: ANP.42 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:E.129, H:E.129, H:H.249, H:E.330 MN.41: 5 residues within 4Å: Chain H: E.131, E.192, E.199 Ligands: MSL.21, ANP.42 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.131, H:E.192, H:E.199 MN.43: 5 residues within 4Å: Chain I: E.129, N.190, E.199 Ligands: MN.45, ANP.46 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:E.129, I:E.199 MN.44: 6 residues within 4Å: Chain I: E.129, H.249, R.316, E.330, R.332 Ligands: ANP.46 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:E.129, I:E.129, I:H.249, I:E.330 MN.45: 6 residues within 4Å: Chain I: E.131, E.192, E.199 Ligands: MSL.19, MN.43, ANP.46 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:E.131, I:E.192, I:E.199 MN.47: 4 residues within 4Å: Chain J: E.129, E.199 Ligands: MN.49, ANP.50 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:E.129, J:E.199 MN.48: 6 residues within 4Å: Chain J: E.129, H.249, R.316, E.330, R.332 Ligands: ANP.50 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.129, J:H.249, J:E.330 MN.49: 6 residues within 4Å: Chain J: E.131, E.192, E.199 Ligands: MSL.20, MN.47, ANP.50 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.131, J:E.192, J:E.199

10 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.4: 22 residues within 4Å: Chain A: W.125, G.127, E.129, S.187, E.199, Q.201, V.202, G.203, P.204, H.249, N.251, Y.252, S.253, R.311, R.316, Y.328, E.330, R.332 Ligands: MN.1, MN.2, MN.3, MSL.12 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.127, A:S.187, A:S.187, A:S.253, A:S.253, A:R.311, A:R.316, A:R.316, A:R.332, B:N.54 ANP.8: 23 residues within 4Å: Chain B: W.125, G.127, E.129, E.131, S.187, E.199, Q.201, V.202, G.203, P.204, H.249, N.251, Y.252, S.253, R.311, R.316, Y.328, E.330, R.332 Ligands: MN.5, MN.6, MN.7, MSL.13 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.127, B:S.187, B:S.187, B:V.202, B:S.253, B:S.253, B:R.311, B:R.311, B:R.316, B:R.316, B:R.332 ANP.22: 23 residues within 4Å: Chain C: W.125, G.127, E.129, E.131, S.187, E.192, E.199, Q.201, G.203, P.204, H.249, N.251, Y.252, S.253, R.311, R.316, Y.328, E.330, R.332 Ligands: MN.9, MN.10, MN.11, MSL.14 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:G.127, C:E.129, C:E.131, C:S.187, C:S.187, C:E.192, C:H.249, C:S.253, C:S.253, C:R.311, C:R.316, C:R.316, C:R.332 Water bridges: C:N.190 ANP.26: 24 residues within 4Å: Chain D: W.125, G.127, E.129, Y.158, S.187, E.192, E.199, Q.201, V.202, G.203, P.204, H.249, N.251, Y.252, S.253, R.311, R.316, Y.328, E.330, R.332 Ligands: MSL.15, MN.23, MN.24, MN.25 13 PLIP interactions: 12 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:G.127, D:Y.158, D:S.187, D:S.187, D:V.202, D:S.253, D:S.253, D:R.311, D:R.316, D:R.316, D:R.332 Water bridges: D:R.311, A:N.54 ANP.30: 22 residues within 4Å: Chain E: W.125, G.127, E.129, S.187, E.192, E.199, Q.201, G.203, P.204, H.249, N.251, Y.252, S.253, R.311, R.316, Y.328, E.330, R.332 Ligands: MSL.16, MN.27, MN.28, MN.29 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:G.127, E:S.187, E:S.187, E:S.187, E:E.192, E:S.253, E:S.253, E:R.311, E:R.316, E:R.316, E:R.332 Water bridges: E:N.251, E:N.251, E:R.311 ANP.34: 22 residues within 4Å: Chain F: W.125, G.127, E.129, S.187, E.192, E.199, Q.201, G.203, P.204, H.249, N.251, Y.252, S.253, R.311, R.316, Y.328, E.330, R.332 Ligands: MSL.18, MN.31, MN.32, MN.33 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:G.127, F:S.187, F:S.187, F:V.202, F:N.251, F:S.253, F:S.253, F:R.311, F:R.316, F:R.316, F:R.332 pi-Stacking: F:Y.328, F:Y.328 ANP.38: 23 residues within 4Å: Chain G: W.125, G.127, E.129, S.187, E.192, E.199, Q.201, V.202, G.203, P.204, H.249, N.251, Y.252, S.253, R.311, R.316, Y.328, E.330, R.332 Ligands: MSL.17, MN.35, MN.36, MN.37 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:G.127, G:S.187, G:S.187, G:V.202, G:S.253, G:S.253, G:R.311, G:R.316, G:R.316, G:R.332 ANP.42: 24 residues within 4Å: Chain H: W.125, G.127, E.129, E.131, S.187, E.192, E.199, Q.201, V.202, G.203, P.204, H.249, N.251, Y.252, S.253, R.311, R.316, Y.328, E.330, R.332 Ligands: MSL.21, MN.39, MN.40, MN.41 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:G.127, H:S.187, H:S.187, H:V.202, H:S.253, H:S.253, H:R.311, H:R.316, H:R.316, H:R.332 ANP.46: 23 residues within 4Å: Chain I: W.125, Y.126, G.127, E.129, E.131, S.187, E.199, Q.201, G.203, P.204, H.249, N.251, Y.252, S.253, R.311, R.316, Y.328, E.330, R.332 Ligands: MSL.19, MN.43, MN.44, MN.45 17 PLIP interactions: 15 interactions with chain I, 2 interactions with chain F Hydrogen bonds: I:G.127, I:E.129, I:E.131, I:E.131, I:S.187, I:S.187, I:H.249, I:S.253, I:S.253, I:R.311, I:R.316, I:R.316, I:R.332 Water bridges: I:N.190, I:Q.201, F:K.36, F:D.56 ANP.50: 22 residues within 4Å: Chain J: W.125, G.127, E.129, E.131, S.187, E.199, Q.201, G.203, P.204, H.249, N.251, Y.252, S.253, R.311, R.316, Y.328, E.330, R.332 Ligands: MSL.20, MN.47, MN.48, MN.49 14 PLIP interactions: 11 interactions with chain J, 3 interactions with chain I Hydrogen bonds: J:G.127, J:S.187, J:E.192, J:V.202, J:S.253, J:S.253, J:R.311, J:R.311, J:R.316, J:R.316, J:R.332, I:N.54 Water bridges: I:K.36, I:K.36

10 x MSL: (2S)-2-AMINO-4-(METHYLSULFONIMIDOYL)BUTANOIC ACID(Non-covalent)

MSL.12: 15 residues within 4Å: Chain A: E.131, Y.158, E.192, N.244, G.245, G.247, H.249, R.291, E.297, T.298, R.311, R.332 Chain B: D.56 Ligands: MN.3, ANP.4 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.244, A:G.245, A:G.247, A:H.296, A:R.311, A:R.332, B:D.56 Water bridges: A:G.245 Salt bridges: A:H.249, A:R.291 MSL.13: 17 residues within 4Å: Chain B: E.131, E.192, V.193, E.199, N.244, G.245, G.247, H.249, R.291, H.296, E.297, T.298, R.311, R.332 Chain C: D.56 Ligands: MN.7, ANP.8 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.197, B:N.244, B:G.245, B:G.247, B:H.296, B:R.311, B:R.332, C:D.56 Salt bridges: B:H.249, B:R.291 MSL.14: 18 residues within 4Å: Chain C: E.131, E.192, V.193, Q.197, E.199, N.244, G.245, G.247, H.249, R.291, H.296, E.297, T.298, R.311, R.332 Chain E: D.56 Ligands: MN.11, ANP.22 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:E.192, C:Q.197, C:N.244, C:G.245, C:G.247, C:H.296, C:R.311, C:R.332, E:D.56 Salt bridges: C:H.249, C:R.291 MSL.15: 18 residues within 4Å: Chain A: D.56 Chain D: E.131, Y.158, E.192, Q.197, E.199, N.244, G.245, G.247, H.249, R.291, H.296, E.297, T.298, R.311, R.332 Ligands: MN.25, ANP.26 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:E.192, D:Q.197, D:N.244, D:G.247, D:H.296, D:R.311, D:R.332 Salt bridges: D:H.249, D:R.291 MSL.16: 16 residues within 4Å: Chain D: D.56 Chain E: E.131, E.192, V.193, N.244, G.245, A.246, G.247, H.249, R.291, E.297, T.298, R.311, R.332 Ligands: MN.29, ANP.30 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:E.192, E:N.244, E:G.245, E:R.311, E:R.332 Salt bridges: E:H.249, E:R.291 MSL.17: 18 residues within 4Å: Chain G: E.131, Y.158, E.192, Q.197, E.199, N.244, G.245, G.247, H.249, R.291, H.296, E.297, T.298, R.311, R.332 Chain H: D.56 Ligands: MN.37, ANP.38 12 PLIP interactions: 11 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:Q.197, G:N.244, G:G.245, G:G.245, G:G.247, G:H.249, G:H.296, G:R.311, G:R.332, H:D.56 Salt bridges: G:H.249, G:R.291 MSL.18: 17 residues within 4Å: Chain F: E.131, E.192, V.193, E.199, N.244, G.245, A.246, G.247, H.249, R.291, E.297, T.298, R.311, R.332 Chain G: D.56 Ligands: MN.33, ANP.34 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:N.244, F:G.245, F:G.245, F:G.247, F:R.311, F:R.332 Water bridges: F:G.245 Salt bridges: F:H.249, F:R.291 MSL.19: 15 residues within 4Å: Chain F: D.56 Chain I: E.131, Y.158, E.192, N.244, G.245, G.247, H.249, R.291, E.297, T.298, R.311, R.332 Ligands: MN.45, ANP.46 8 PLIP interactions: 8 interactions with chain I Hydrogen bonds: I:N.244, I:G.245, I:G.247, I:H.296, I:R.311, I:R.332 Salt bridges: I:H.249, I:R.291 MSL.20: 16 residues within 4Å: Chain I: D.56 Chain J: E.131, Y.158, E.192, E.199, N.244, G.245, G.247, H.249, R.291, E.297, T.298, R.311, R.332 Ligands: MN.49, ANP.50 9 PLIP interactions: 9 interactions with chain J Hydrogen bonds: J:N.244, J:G.245, J:G.245, J:G.245, J:G.247, J:R.311, J:R.332 Salt bridges: J:H.249, J:R.291 MSL.21: 16 residues within 4Å: Chain H: E.131, Y.158, E.192, E.199, N.244, G.245, A.246, G.247, H.249, R.291, E.297, R.311, R.332 Chain J: D.56 Ligands: MN.41, ANP.42 10 PLIP interactions: 9 interactions with chain H, 1 interactions with chain J Hydrogen bonds: H:N.244, H:G.245, H:G.245, H:G.247, H:H.249, H:R.311, H:R.332, J:D.56 Salt bridges: H:H.249, H:R.291

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Unno, H. et al., Atomic Structure of Plant Glutamine Synthetase: A KEY ENZYME FOR PLANT PRODUCTIVITY. J.Biol.Chem. (2006)

Release Date

2006-07-18

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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