SMTL ID : 8ool.1

Glutamine synthetase from Methanothermococcus thermolithotrophicus with TbXo4 at a resolution of 1.65 A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-12-mer

Ligands

90 x TB: TERBIUM(III) ION(Non-covalent)(Non-functional Binders)

TB.1: 1 residues within 4Å: Chain A: E.122 Ligand excluded by PLIP TB.2: 3 residues within 4Å: Chain A: E.139, E.194, E.201 Ligand excluded by PLIP TB.3: 1 residues within 4Å: Chain A: E.424 Ligand excluded by PLIP TB.4: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.5: 1 residues within 4Å: Chain A: D.158 Ligand excluded by PLIP TB.6: 1 residues within 4Å: Chain A: E.391 Ligand excluded by PLIP TB.8: 1 residues within 4Å: Chain B: E.122 Ligand excluded by PLIP TB.9: 2 residues within 4Å: Chain B: K.288, E.391 Ligand excluded by PLIP TB.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.11: 1 residues within 4Å: Chain B: E.424 Ligand excluded by PLIP TB.12: 1 residues within 4Å: Chain B: D.158 Ligand excluded by PLIP TB.13: 3 residues within 4Å: Chain B: E.139, E.194, E.201 Ligand excluded by PLIP TB.14: 1 residues within 4Å: Chain B: E.260 Ligand excluded by PLIP TB.16: 1 residues within 4Å: Chain C: E.424 Ligand excluded by PLIP TB.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.18: 3 residues within 4Å: Chain C: E.139, E.194, E.201 Ligand excluded by PLIP TB.19: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.20: 1 residues within 4Å: Chain C: D.408 Ligand excluded by PLIP TB.21: 1 residues within 4Å: Chain C: D.158 Ligand excluded by PLIP TB.22: 1 residues within 4Å: Chain C: E.391 Ligand excluded by PLIP TB.23: 1 residues within 4Å: Chain C: E.260 Ligand excluded by PLIP TB.26: 1 residues within 4Å: Chain D: E.122 Ligand excluded by PLIP TB.27: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.28: 1 residues within 4Å: Chain D: E.424 Ligand excluded by PLIP TB.29: 1 residues within 4Å: Chain D: D.158 Ligand excluded by PLIP TB.30: 3 residues within 4Å: Chain D: E.139, E.194, E.201 Ligand excluded by PLIP TB.31: 1 residues within 4Å: Chain D: E.391 Ligand excluded by PLIP TB.32: 1 residues within 4Å: Chain D: E.260 Ligand excluded by PLIP TB.34: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.35: 1 residues within 4Å: Chain E: E.424 Ligand excluded by PLIP TB.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.37: 1 residues within 4Å: Chain E: D.158 Ligand excluded by PLIP TB.38: 1 residues within 4Å: Chain E: N.129 Ligand excluded by PLIP TB.39: 3 residues within 4Å: Chain E: E.139, E.194, E.201 Ligand excluded by PLIP TB.40: 1 residues within 4Å: Chain E: E.391 Ligand excluded by PLIP TB.41: 1 residues within 4Å: Chain E: E.260 Ligand excluded by PLIP TB.43: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.44: 1 residues within 4Å: Chain F: E.260 Ligand excluded by PLIP TB.45: 1 residues within 4Å: Chain F: E.424 Ligand excluded by PLIP TB.46: 3 residues within 4Å: Chain F: E.139, E.194, E.201 Ligand excluded by PLIP TB.47: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.48: 1 residues within 4Å: Chain F: D.158 Ligand excluded by PLIP TB.49: 1 residues within 4Å: Chain F: D.158 Ligand excluded by PLIP TB.50: 1 residues within 4Å: Chain F: D.408 Ligand excluded by PLIP TB.51: 1 residues within 4Å: Chain F: E.391 Ligand excluded by PLIP TB.53: 1 residues within 4Å: Chain G: E.122 Ligand excluded by PLIP TB.54: 3 residues within 4Å: Chain G: E.139, E.194, E.201 Ligand excluded by PLIP TB.55: 1 residues within 4Å: Chain G: E.424 Ligand excluded by PLIP TB.56: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.57: 1 residues within 4Å: Chain G: D.158 Ligand excluded by PLIP TB.58: 1 residues within 4Å: Chain G: E.391 Ligand excluded by PLIP TB.60: 1 residues within 4Å: Chain H: E.122 Ligand excluded by PLIP TB.61: 2 residues within 4Å: Chain H: K.288, E.391 Ligand excluded by PLIP TB.62: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.63: 1 residues within 4Å: Chain H: E.424 Ligand excluded by PLIP TB.64: 1 residues within 4Å: Chain H: D.158 Ligand excluded by PLIP TB.65: 3 residues within 4Å: Chain H: E.139, E.194, E.201 Ligand excluded by PLIP TB.66: 1 residues within 4Å: Chain H: E.260 Ligand excluded by PLIP TB.68: 1 residues within 4Å: Chain I: E.424 Ligand excluded by PLIP TB.69: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.70: 3 residues within 4Å: Chain I: E.139, E.194, E.201 Ligand excluded by PLIP TB.71: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.72: 1 residues within 4Å: Chain I: D.408 Ligand excluded by PLIP TB.73: 1 residues within 4Å: Chain I: D.158 Ligand excluded by PLIP TB.74: 1 residues within 4Å: Chain I: E.391 Ligand excluded by PLIP TB.75: 1 residues within 4Å: Chain I: E.260 Ligand excluded by PLIP TB.78: 1 residues within 4Å: Chain J: E.122 Ligand excluded by PLIP TB.79: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.80: 1 residues within 4Å: Chain J: E.424 Ligand excluded by PLIP TB.81: 1 residues within 4Å: Chain J: D.158 Ligand excluded by PLIP TB.82: 3 residues within 4Å: Chain J: E.139, E.194, E.201 Ligand excluded by PLIP TB.83: 1 residues within 4Å: Chain J: E.391 Ligand excluded by PLIP TB.84: 1 residues within 4Å: Chain J: E.260 Ligand excluded by PLIP TB.86: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.87: 1 residues within 4Å: Chain K: E.424 Ligand excluded by PLIP TB.88: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.89: 1 residues within 4Å: Chain K: D.158 Ligand excluded by PLIP TB.90: 1 residues within 4Å: Chain K: N.129 Ligand excluded by PLIP TB.91: 3 residues within 4Å: Chain K: E.139, E.194, E.201 Ligand excluded by PLIP TB.92: 1 residues within 4Å: Chain K: E.391 Ligand excluded by PLIP TB.93: 1 residues within 4Å: Chain K: E.260 Ligand excluded by PLIP TB.95: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.96: 1 residues within 4Å: Chain L: E.260 Ligand excluded by PLIP TB.97: 1 residues within 4Å: Chain L: E.424 Ligand excluded by PLIP TB.98: 3 residues within 4Å: Chain L: E.139, E.194, E.201 Ligand excluded by PLIP TB.99: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.100: 1 residues within 4Å: Chain L: D.158 Ligand excluded by PLIP TB.101: 1 residues within 4Å: Chain L: D.158 Ligand excluded by PLIP TB.102: 1 residues within 4Å: Chain L: D.408 Ligand excluded by PLIP TB.103: 1 residues within 4Å: Chain L: E.391 Ligand excluded by PLIP

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 5 residues within 4Å: Chain A: H.250, R.303, E.309, P.311, R.340 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.309 Water bridges: A:E.139, A:N.245, A:G.246, A:G.248, A:G.248 Salt bridges: A:H.250, A:R.303 SO4.15: 5 residues within 4Å: Chain B: H.250, R.303, E.309, P.311, R.340 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.309 Water bridges: B:E.139, B:N.245, B:N.245, B:G.248, B:G.248 Salt bridges: B:H.250, B:R.303 SO4.24: 5 residues within 4Å: Chain C: H.250, R.303, E.309, P.311, R.340 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:E.309 Water bridges: C:E.139, C:N.245, C:G.246, C:G.248, C:G.248 Salt bridges: C:H.250, C:R.303 SO4.33: 5 residues within 4Å: Chain D: H.250, R.303, E.309, P.311, R.340 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.309 Water bridges: D:E.139, D:G.246, D:G.248, D:G.248 Salt bridges: D:H.250, D:R.303 SO4.42: 5 residues within 4Å: Chain E: H.250, R.303, E.309, P.311, R.340 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:E.309 Water bridges: E:E.139, E:E.139, E:N.245, E:G.246, E:G.248 Salt bridges: E:H.250, E:R.303 SO4.52: 5 residues within 4Å: Chain F: H.250, R.303, E.309, P.311, R.340 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:E.309 Water bridges: F:E.139, F:G.246, F:G.248, F:G.248 Salt bridges: F:H.250, F:R.303 SO4.59: 5 residues within 4Å: Chain G: H.250, R.303, E.309, P.311, R.340 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:E.309 Water bridges: G:E.139, G:N.245, G:G.246, G:G.248, G:G.248 Salt bridges: G:H.250, G:R.303 SO4.67: 5 residues within 4Å: Chain H: H.250, R.303, E.309, P.311, R.340 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:E.309 Water bridges: H:E.139, H:N.245, H:N.245, H:G.248, H:G.248 Salt bridges: H:H.250, H:R.303 SO4.76: 5 residues within 4Å: Chain I: H.250, R.303, E.309, P.311, R.340 8 PLIP interactions: 8 interactions with chain I Hydrogen bonds: I:E.309 Water bridges: I:E.139, I:N.245, I:G.246, I:G.248, I:G.248 Salt bridges: I:H.250, I:R.303 SO4.85: 5 residues within 4Å: Chain J: H.250, R.303, E.309, P.311, R.340 7 PLIP interactions: 7 interactions with chain J Hydrogen bonds: J:E.309 Water bridges: J:E.139, J:G.246, J:G.248, J:G.248 Salt bridges: J:H.250, J:R.303 SO4.94: 5 residues within 4Å: Chain K: H.250, R.303, E.309, P.311, R.340 8 PLIP interactions: 8 interactions with chain K Hydrogen bonds: K:E.309 Water bridges: K:E.139, K:E.139, K:N.245, K:G.246, K:G.248 Salt bridges: K:H.250, K:R.303 SO4.104: 5 residues within 4Å: Chain L: H.250, R.303, E.309, P.311, R.340 7 PLIP interactions: 7 interactions with chain L Hydrogen bonds: L:E.309 Water bridges: L:E.139, L:G.246, L:G.248, L:G.248 Salt bridges: L:H.250, L:R.303

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.25: 4 residues within 4Å: Chain D: E.228, Q.229, H.230, G.231 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.230 Water bridges: D:E.228, D:G.231 GOL.77: 4 residues within 4Å: Chain J: E.228, Q.229, H.230, G.231 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:H.230 Water bridges: J:E.228, J:G.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muller, M.C. et al., Differences in regulation mechanisms of glutamine synthetases from methanogenic archaea unveiled by structural investigations. Commun Biol (2024)

Release Date

2024-01-24

Peptides

Glutamine synthetase from Methanothermococcus thermolithotrophicus: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
A

H
B

I
C

J
D

K
E

L
F

Glutamine synthetase from Methanothermococcus thermolithotrophicus

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