SMTL ID : 8oon.1

Glutamine synthetase from Methanothermococcus thermolithotrophicus at a resolution of 2.43 A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

homo-12-mer

Ligands

70 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: R.434 Chain G: K.302, A.395, N.396, F.433 Ligand excluded by PLIP EDO.2: 6 residues within 4Å: Chain A: G.135, E.137, D.203, F.204, F.206, H.252 Ligand excluded by PLIP EDO.3: 2 residues within 4Å: Chain A: G.246, R.303 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: K.239, M.244, N.245 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: K.144, A.156, D.158, E.169 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: D.431, R.434, T.435 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: E.420, L.423, E.424, N.427 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: P.240, F.241, F.242 Chain G: V.437 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: M.121, D.208, L.210 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain B: E.139, E.194, Q.199, N.245, G.246, G.248 Ligands: GOL.11 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain B: L.142, A.156, D.157, E.169, A.170, H.200, L.232 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain B: K.224, K.233, A.234 Chain L: L.446, K.447 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain B: P.240, F.241, F.242 Chain L: V.437, T.442 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain B: D.431, T.435 Chain L: P.306 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain B: Y.301, K.302, A.395, N.396 Chain L: R.434 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain C: G.246, H.250, R.303 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain C: I.26, L.27, I.293, P.296, C.346, N.347, F.422 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain C: L.27, T.297, S.345, K.426 Chain K: Y.445 Ligand excluded by PLIP EDO.20: 1 residues within 4Å: Chain C: R.321 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain C: G.135, P.136, E.137, F.204, H.252, R.336 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain C: V.298, Y.301, K.302, N.396, W.430, F.433 Chain K: R.434 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain C: K.224, K.233, A.234 Chain K: L.446, K.447 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain C: K.144, H.230, G.231 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain C: E.139, E.194, E.201, H.250 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain D: D.439, T.442, T.443 Chain J: K.152 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain D: V.437, T.442 Chain J: P.240, F.241, F.242 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain D: V.298, Y.301, K.302, N.396, L.397, W.430, F.433 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain D: W.440, T.443, A.444 Ligand excluded by PLIP EDO.30: 7 residues within 4Å: Chain D: G.135, P.136, E.137, D.203, F.204, H.252, R.336 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain E: E.139, N.245, G.246, G.248, R.303 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain E: V.298, K.302, N.396, F.433 Chain I: W.430 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain E: K.144, P.155, A.156, D.157, D.158, E.169 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain E: G.135, E.137, D.203, F.204, F.206, H.252 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain F: I.154, P.155, D.158, P.197 Ligand excluded by PLIP EDO.39: 6 residues within 4Å: Chain F: L.27, T.297, S.345, K.426, E.429 Chain H: Y.445 Ligand excluded by PLIP EDO.40: 5 residues within 4Å: Chain A: K.302, A.395, N.396, F.433 Chain G: R.434 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain G: G.135, E.137, D.203, F.204, F.206, H.252 Ligand excluded by PLIP EDO.42: 2 residues within 4Å: Chain G: G.246, R.303 Ligand excluded by PLIP EDO.43: 3 residues within 4Å: Chain G: K.239, M.244, N.245 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain G: K.144, A.156, D.158, E.169 Ligand excluded by PLIP EDO.45: 3 residues within 4Å: Chain G: D.431, R.434, T.435 Ligand excluded by PLIP EDO.46: 4 residues within 4Å: Chain G: E.420, L.423, E.424, N.427 Ligand excluded by PLIP EDO.47: 4 residues within 4Å: Chain A: V.437 Chain G: P.240, F.241, F.242 Ligand excluded by PLIP EDO.48: 3 residues within 4Å: Chain G: M.121, D.208, L.210 Ligand excluded by PLIP EDO.49: 7 residues within 4Å: Chain H: E.139, E.194, Q.199, N.245, G.246, G.248 Ligands: GOL.50 Ligand excluded by PLIP EDO.51: 7 residues within 4Å: Chain H: L.142, A.156, D.157, E.169, A.170, H.200, L.232 Ligand excluded by PLIP EDO.52: 5 residues within 4Å: Chain F: L.446, K.447 Chain H: K.224, K.233, A.234 Ligand excluded by PLIP EDO.53: 5 residues within 4Å: Chain F: V.437, T.442 Chain H: P.240, F.241, F.242 Ligand excluded by PLIP EDO.54: 3 residues within 4Å: Chain F: P.306 Chain H: D.431, T.435 Ligand excluded by PLIP EDO.55: 5 residues within 4Å: Chain F: R.434 Chain H: Y.301, K.302, A.395, N.396 Ligand excluded by PLIP EDO.56: 3 residues within 4Å: Chain I: G.246, H.250, R.303 Ligand excluded by PLIP EDO.57: 7 residues within 4Å: Chain I: I.26, L.27, I.293, P.296, C.346, N.347, F.422 Ligand excluded by PLIP EDO.58: 5 residues within 4Å: Chain E: Y.445 Chain I: L.27, T.297, S.345, K.426 Ligand excluded by PLIP EDO.59: 1 residues within 4Å: Chain I: R.321 Ligand excluded by PLIP EDO.60: 6 residues within 4Å: Chain I: G.135, P.136, E.137, F.204, H.252, R.336 Ligand excluded by PLIP EDO.61: 7 residues within 4Å: Chain E: R.434 Chain I: V.298, Y.301, K.302, N.396, W.430, F.433 Ligand excluded by PLIP EDO.62: 5 residues within 4Å: Chain E: L.446, K.447 Chain I: K.224, K.233, A.234 Ligand excluded by PLIP EDO.63: 3 residues within 4Å: Chain I: K.144, H.230, G.231 Ligand excluded by PLIP EDO.64: 4 residues within 4Å: Chain I: E.139, E.194, E.201, H.250 Ligand excluded by PLIP EDO.65: 4 residues within 4Å: Chain D: K.152 Chain J: D.439, T.442, T.443 Ligand excluded by PLIP EDO.66: 5 residues within 4Å: Chain D: P.240, F.241, F.242 Chain J: V.437, T.442 Ligand excluded by PLIP EDO.67: 7 residues within 4Å: Chain J: V.298, Y.301, K.302, N.396, L.397, W.430, F.433 Ligand excluded by PLIP EDO.68: 3 residues within 4Å: Chain J: W.440, T.443, A.444 Ligand excluded by PLIP EDO.69: 7 residues within 4Å: Chain J: G.135, P.136, E.137, D.203, F.204, H.252, R.336 Ligand excluded by PLIP EDO.71: 5 residues within 4Å: Chain K: E.139, N.245, G.246, G.248, R.303 Ligand excluded by PLIP EDO.72: 5 residues within 4Å: Chain C: W.430 Chain K: V.298, K.302, N.396, F.433 Ligand excluded by PLIP EDO.73: 6 residues within 4Å: Chain K: K.144, P.155, A.156, D.157, D.158, E.169 Ligand excluded by PLIP EDO.74: 6 residues within 4Å: Chain K: G.135, E.137, D.203, F.204, F.206, H.252 Ligand excluded by PLIP EDO.76: 4 residues within 4Å: Chain L: I.154, P.155, D.158, P.197 Ligand excluded by PLIP EDO.78: 6 residues within 4Å: Chain B: Y.445 Chain L: L.27, T.297, S.345, K.426, E.429 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 6 residues within 4Å: Chain B: N.245, G.246, H.250, R.303, R.340 Ligands: EDO.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.245, B:G.246, B:R.303, B:R.340 GOL.38: 5 residues within 4Å: Chain F: E.139, N.245, G.246, G.248, R.303 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:E.139, F:G.246, F:R.303 GOL.50: 6 residues within 4Å: Chain H: N.245, G.246, H.250, R.303, R.340 Ligands: EDO.49 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:N.245, H:G.246, H:R.303, H:R.340 GOL.77: 5 residues within 4Å: Chain L: E.139, N.245, G.246, G.248, R.303 3 PLIP interactions: 3 interactions with chain L Hydrogen bonds: L:E.139, L:G.246, L:R.303

4 x NA: SODIUM ION(Non-functional Binders)

NA.31: 1 residues within 4Å: Chain D: E.420 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.420 NA.36: 1 residues within 4Å: Chain E: E.424 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.424 NA.70: 1 residues within 4Å: Chain J: E.420 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:E.420, J:E.420 NA.75: 1 residues within 4Å: Chain K: E.424 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:E.424

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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