SMTL ID : 8s59.1

Cryo-EM structure of the active dodecameric Methanosarcina mazei glutamine synthetase.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

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

AKG.1: 9 residues within 4Å: Chain A: F.23, R.25, A.39, R.86, V.92 Chain F: Q.168, R.171, R.172, S.188 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain F Hydrophobic interactions: A:F.23, F:R.171, F:R.172 Water bridges: A:R.25, F:R.171 Salt bridges: A:R.25, A:R.25, A:R.86, F:R.171, F:R.172 AKG.2: 9 residues within 4Å: Chain B: F.23, R.25, A.39, R.86, V.92 Chain L: Q.168, R.171, R.172, S.188 12 PLIP interactions: 6 interactions with chain L, 6 interactions with chain B Hydrophobic interactions: L:R.171, L:R.172, B:F.23 Hydrogen bonds: L:S.188, B:R.25 Water bridges: L:R.171, B:R.25 Salt bridges: L:R.171, L:R.172, B:R.25, B:R.25, B:R.86 AKG.3: 9 residues within 4Å: Chain C: F.23, R.25, A.39, R.86, V.92 Chain D: Q.168, R.171, R.172, S.188 11 PLIP interactions: 6 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:R.171, D:R.172, C:F.23 Hydrogen bonds: D:S.188 Water bridges: D:R.171, C:R.25 Salt bridges: D:R.171, D:R.172, C:R.25, C:R.25, C:R.86 AKG.4: 9 residues within 4Å: Chain B: Q.168, R.171, R.172, S.188 Chain D: F.23, R.25, A.39, R.86, V.92 11 PLIP interactions: 5 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:F.23, B:R.171, B:R.172 Water bridges: D:R.25, B:R.171 Salt bridges: D:R.25, D:R.25, D:R.86, B:R.171, B:R.172 Hydrogen bonds: B:S.188 AKG.5: 9 residues within 4Å: Chain A: Q.168, R.171, R.172, S.188 Chain E: F.23, R.25, A.39, R.86, V.92 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain E Hydrophobic interactions: A:R.171, A:R.172, E:F.23 Water bridges: A:R.171, E:R.25 Salt bridges: A:R.171, A:R.172, E:R.25, E:R.25, E:R.86 AKG.6: 9 residues within 4Å: Chain F: F.23, R.25, A.39, R.86, V.92 Chain J: Q.168, R.171, R.172, S.188 11 PLIP interactions: 6 interactions with chain F, 5 interactions with chain J Hydrophobic interactions: F:F.23, J:R.171, J:R.172 Hydrogen bonds: F:R.25 Water bridges: F:R.25, J:R.171 Salt bridges: F:R.25, F:R.25, F:R.86, J:R.171, J:R.172 AKG.7: 9 residues within 4Å: Chain G: F.23, R.25, A.39, R.86, V.92 Chain H: Q.168, R.171, R.172, S.188 11 PLIP interactions: 5 interactions with chain G, 6 interactions with chain H Hydrophobic interactions: G:F.23, H:R.171, H:R.172 Water bridges: G:R.25, H:R.171 Salt bridges: G:R.25, G:R.25, G:R.86, H:R.171, H:R.172 Hydrogen bonds: H:S.188 AKG.8: 9 residues within 4Å: Chain C: Q.168, R.171, R.172, S.188 Chain H: F.23, R.25, A.39, R.86, V.92 11 PLIP interactions: 5 interactions with chain H, 6 interactions with chain C Hydrophobic interactions: H:F.23, C:R.171, C:R.172 Water bridges: H:R.25, C:R.171 Salt bridges: H:R.25, H:R.25, H:R.86, C:R.171, C:R.172 Hydrogen bonds: C:S.188 AKG.9: 9 residues within 4Å: Chain I: F.23, R.25, A.39, R.86, V.92 Chain K: Q.168, R.171, R.172, S.188 10 PLIP interactions: 5 interactions with chain I, 5 interactions with chain K Hydrophobic interactions: I:F.23, K:R.171, K:R.172 Water bridges: I:A.39, K:R.171 Salt bridges: I:R.25, I:R.25, I:R.86, K:R.171, K:R.172 AKG.10: 9 residues within 4Å: Chain I: Q.168, R.171, R.172, S.188 Chain J: F.23, R.25, A.39, R.86, V.92 11 PLIP interactions: 5 interactions with chain J, 6 interactions with chain I Hydrophobic interactions: J:F.23, I:R.171, I:R.172 Water bridges: J:R.25, I:R.171 Salt bridges: J:R.25, J:R.25, J:R.86, I:R.171, I:R.172 Hydrogen bonds: I:Q.168 AKG.11: 9 residues within 4Å: Chain E: Q.168, R.171, R.172, S.188 Chain K: F.23, R.25, A.39, R.86, V.92 11 PLIP interactions: 5 interactions with chain K, 6 interactions with chain E Hydrophobic interactions: K:F.23, E:R.171, E:R.172 Water bridges: K:R.25, E:R.171 Salt bridges: K:R.25, K:R.25, K:R.86, E:R.171, E:R.172 Hydrogen bonds: E:Q.168 AKG.12: 9 residues within 4Å: Chain G: Q.168, R.171, R.172, S.188 Chain L: F.23, R.25, A.39, R.86, V.92 11 PLIP interactions: 5 interactions with chain L, 6 interactions with chain G Hydrophobic interactions: L:F.23, G:R.171, G:R.172 Water bridges: L:R.25, G:R.171 Salt bridges: L:R.25, L:R.25, L:R.86, G:R.171, G:R.172 Hydrogen bonds: G:S.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, A. et al., Cryo-EM structure of the active dodecameric Methanosarcina mazei glutamine synthetase. Elife (2024)

Release Date

2025-01-08

Peptides

Glutamine synthetase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
D

C
A

D
B

E
C

F
L

G
M

H
P

I
Q

J
V

K
X

L
Y

Glutamine synthetase