SMTL ID : 8ooq.1 (1 other biounit)

Glutamine synthetase from Methanothermococcus thermolithotrophicus in complex with 2-oxoglutarate and Mg at 2.91 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.91 Å

Oligo State

homo-12-mer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: K.302, A.395, N.396, W.430, F.433 Chain E: F.433 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.302, A:A.395 EDO.9: 6 residues within 4Å: Chain A: F.433 Chain E: K.302, A.395, N.396, F.433 Ligands: EDO.1 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:A.395, E:N.396 EDO.11: 5 residues within 4Å: Chain B: R.88 Chain F: E.165, E.169, P.171, D.172 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:R.88, F:D.172 EDO.14: 3 residues within 4Å: Chain G: R.88 Chain H: P.171, D.172 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:R.88 EDO.21: 5 residues within 4Å: Chain K: E.70, D.72, M.73, T.103, T.104 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:D.72, K:T.104, K:T.104

7 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 2 residues within 4Å: Chain A: I.448 Chain E: K.220 No protein-ligand interaction detected (PLIP) MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: E.139, E.194, E.201 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.139, B:E.194, B:E.201 MG.12: 1 residues within 4Å: Chain F: Y.56 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain G: L.55 Chain H: A.190 No protein-ligand interaction detected (PLIP) MG.19: 4 residues within 4Å: Chain J: E.137, E.139, E.194, E.201 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.139, J:E.194, J:E.201 MG.22: 5 residues within 4Å: Chain K: E.137, H.250, R.321, R.326, E.338 No protein-ligand interaction detected (PLIP)

12 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.3: 9 residues within 4Å: Chain A: P.171, R.174, R.175, S.191 Chain L: F.18, R.20, A.34, R.88, V.94 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain L Hydrophobic interactions: A:R.175, L:F.18, L:A.34 Hydrogen bonds: A:P.171, L:R.20 Salt bridges: A:R.174, A:R.175, L:R.20, L:R.20, L:R.88 AKG.6: 9 residues within 4Å: Chain B: P.171, R.174, R.175, S.191 Chain H: F.18, R.20, A.34, R.88, V.94 10 PLIP interactions: 6 interactions with chain H, 4 interactions with chain B Hydrophobic interactions: H:F.18, H:A.34, B:R.175 Hydrogen bonds: H:R.20, B:S.191 Salt bridges: H:R.20, H:R.20, H:R.88, B:R.174, B:R.175 AKG.7: 9 residues within 4Å: Chain C: P.171, R.174, R.175, S.191 Chain J: F.18, R.20, A.34, R.88, V.94 9 PLIP interactions: 5 interactions with chain J, 4 interactions with chain C Hydrophobic interactions: J:F.18, J:A.34, C:R.175 Hydrogen bonds: J:R.20, C:P.171 Salt bridges: J:R.20, J:R.88, C:R.174, C:R.175 AKG.8: 9 residues within 4Å: Chain D: P.171, R.174, R.175, S.191 Chain F: F.18, R.20, A.34, R.88, V.94 8 PLIP interactions: 4 interactions with chain F, 4 interactions with chain D Hydrophobic interactions: F:A.34, D:R.175 Salt bridges: F:R.20, F:R.20, F:R.88, D:R.174, D:R.175 Hydrogen bonds: D:S.191 AKG.10: 9 residues within 4Å: Chain D: F.18, R.20, A.34, R.88, V.94 Chain E: P.171, R.174, R.175, S.191 9 PLIP interactions: 4 interactions with chain E, 5 interactions with chain D Hydrophobic interactions: E:R.175, D:F.18, D:A.34 Hydrogen bonds: E:S.191 Salt bridges: E:R.174, E:R.175, D:R.20, D:R.20, D:R.88 AKG.13: 9 residues within 4Å: Chain B: F.18, R.20, A.34, R.88, V.94 Chain F: P.171, R.174, R.175, S.191 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain F Hydrophobic interactions: B:F.18, B:A.34, F:R.175 Hydrogen bonds: B:R.20, F:S.191 Salt bridges: B:R.20, B:R.20, B:R.88, F:R.174, F:R.175 AKG.15: 9 residues within 4Å: Chain E: F.18, R.20, A.34, R.88, V.94 Chain G: P.171, R.174, R.175, S.191 9 PLIP interactions: 4 interactions with chain G, 5 interactions with chain E Hydrophobic interactions: G:R.175, E:F.18, E:A.34 Hydrogen bonds: G:S.191, E:R.20 Salt bridges: G:R.174, G:R.175, E:R.20, E:R.88 AKG.17: 10 residues within 4Å: Chain G: F.18, R.20, A.34, R.88, V.94 Chain H: P.171, R.174, R.175, S.191, H.192 9 PLIP interactions: 5 interactions with chain G, 4 interactions with chain H Hydrophobic interactions: G:A.34, H:R.175 Hydrogen bonds: G:R.20, H:P.171 Salt bridges: G:R.20, G:R.20, G:R.88, H:R.174, H:R.175 AKG.18: 9 residues within 4Å: Chain C: F.18, R.20, A.34, R.88, V.94 Chain I: P.171, R.174, R.175, S.191 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain I Hydrophobic interactions: C:F.18, C:A.34, I:R.175 Hydrogen bonds: C:R.20, I:P.171 Salt bridges: C:R.20, C:R.20, C:R.88, I:R.174, I:R.175 AKG.20: 9 residues within 4Å: Chain A: F.18, R.20, A.34, R.88, V.94 Chain J: P.171, R.174, R.175, S.191 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain J Hydrophobic interactions: A:F.18, A:A.34, J:R.175 Hydrogen bonds: A:R.20, J:P.171 Salt bridges: A:R.20, A:R.20, A:R.88, J:R.174, J:R.175 AKG.23: 9 residues within 4Å: Chain I: F.18, R.20, A.34, R.88, V.94 Chain K: P.171, R.174, R.175, S.191 10 PLIP interactions: 6 interactions with chain I, 4 interactions with chain K Hydrophobic interactions: I:F.18, I:A.34, K:R.175 Hydrogen bonds: I:R.20, K:P.171 Salt bridges: I:R.20, I:R.20, I:R.88, K:R.174, K:R.175 AKG.24: 9 residues within 4Å: Chain K: F.18, R.20, A.34, R.88, V.94 Chain L: P.171, R.174, R.175, S.191 10 PLIP interactions: 4 interactions with chain L, 6 interactions with chain K Hydrophobic interactions: L:R.175, K:F.18, K:A.34 Hydrogen bonds: L:S.191, K:R.20 Salt bridges: L:R.174, L:R.175, K:R.20, K:R.20, K:R.88

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
G

H
H

I
I

J
J

K
K

L
L

Glutamine synthetase from Methanothermococcus thermolithotrophicus

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