- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.15 Å
- Oligo State
- homo-12-mer
- Ligands
- 26 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 10 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.2: 6 residues within 4Å:- Chain A: K.152, Y.153, I.154, P.240, F.241, F.242
3 PLIP interactions:1 interactions with chain A, 2 interactions with chain E- Hydrogen bonds: A:F.242
- Water bridges: E:V.437, E:V.437
PEG.4: 4 residues within 4Å:- Chain A: H.187, K.205, D.207
- Chain L: K.42
3 PLIP interactions:2 interactions with chain L, 1 interactions with chain A- Hydrogen bonds: L:K.42, L:K.42, A:K.205
PEG.24: 7 residues within 4Å:- Chain D: Y.161, F.162, H.192, D.203
- Chain F: L.55, Y.56
- Ligands: ATP.27
4 PLIP interactions:2 interactions with chain F, 2 interactions with chain D- Water bridges: F:Y.56, F:D.58, D:E.194
- Hydrogen bonds: D:Y.161
PEG.25: 7 residues within 4Å:- Chain D: K.144, I.154, P.155, A.156, D.157, D.158, E.169
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:K.144, D:E.169
- Water bridges: D:D.158
PEG.40: 5 residues within 4Å:- Chain E: P.89
- Chain G: D.172, R.175, D.176, F.179
3 PLIP interactions:1 interactions with chain E, 2 interactions with chain G- Hydrogen bonds: E:E.91, G:D.172, G:R.175
PEG.41: 3 residues within 4Å:- Chain G: E.429
- Chain L: A.444
- Ligands: PEG.42
2 PLIP interactions:1 interactions with chain L, 1 interactions with chain G- Hydrogen bonds: L:A.444
- Water bridges: G:E.429
PEG.42: 9 residues within 4Å:- Chain G: L.27, G.28, T.297, S.345, K.426, E.429
- Chain L: Y.445, I.448
- Ligands: PEG.41
4 PLIP interactions:4 interactions with chain G- Hydrogen bonds: G:K.220, G:K.220, G:K.426, G:E.429
PEG.43: 6 residues within 4Å:- Chain G: N.396, W.430, F.433
- Chain L: N.396, W.430, F.433
7 PLIP interactions:4 interactions with chain L, 3 interactions with chain G- Water bridges: L:A.395, L:A.395, L:N.396, L:R.434, G:V.298, G:A.395, G:N.396
PEG.55: 6 residues within 4Å:- Chain D: F.242
- Chain J: S.432, T.435, S.436, V.437
- Ligands: PG4.22
5 PLIP interactions:4 interactions with chain J, 1 interactions with chain D- Hydrogen bonds: J:S.432, J:V.437, J:V.437
- Water bridges: J:S.436, D:F.242
PEG.60: 9 residues within 4Å:- Chain K: F.186, H.187, F.204, K.205, F.206, D.207, K.211, T.212, S.215
6 PLIP interactions:6 interactions with chain K- Hydrogen bonds: K:V.134, K:H.187, K:H.187, K:K.205, K:D.207, K:S.215
- 1 x GOL: GLYCEROL(Non-functional Binders)
- 12 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
ATP.8: 18 residues within 4Å:- Chain A: F.133, G.135, E.137, E.189, E.201, D.203, F.204, K.205, F.206, H.250, H.252, S.254, R.321, R.326, K.333, T.335, R.336, E.338
27 PLIP interactions:25 interactions with chain A, 2 interactions with chain L- Hydrogen bonds: A:E.189, A:F.206, A:H.250, A:S.254, A:S.254, A:R.321
- Water bridges: A:P.136, A:E.201, A:E.201, A:D.203, A:D.203, A:F.204, A:R.326, A:R.340, A:R.340, L:Y.56, L:F.57
- Salt bridges: A:H.252, A:H.252, A:H.252, A:R.321, A:R.326, A:R.326, A:R.336
- pi-Stacking: A:F.206, A:F.206
- pi-Cation interactions: A:R.336
ATP.15: 20 residues within 4Å:- Chain B: F.133, G.135, E.137, E.189, E.201, D.203, F.204, K.205, F.206, H.250, H.252, Q.253, S.254, R.321, R.326, K.333, T.335, R.336, E.338
- Ligands: MG.14
25 PLIP interactions:24 interactions with chain B, 1 interactions with chain H- Hydrogen bonds: B:E.189, B:E.201, B:F.206, B:H.250, B:S.254, B:S.254, B:R.321
- Water bridges: B:P.136, B:E.137, B:E.137, B:F.204, B:T.335, B:R.340, H:D.58
- Salt bridges: B:H.252, B:H.252, B:H.252, B:R.321, B:R.326, B:R.326, B:R.336, B:R.336
- pi-Stacking: B:F.206, B:F.206
- pi-Cation interactions: B:R.336
ATP.20: 20 residues within 4Å:- Chain C: F.133, G.135, E.137, E.189, E.201, D.203, F.204, K.205, F.206, H.250, H.252, Q.253, S.254, R.321, R.326, K.333, G.334, T.335, R.336, E.338
29 PLIP interactions:26 interactions with chain C, 3 interactions with chain J- Hydrogen bonds: C:E.189, C:E.201, C:F.206, C:S.254, C:S.254, C:R.336
- Water bridges: C:E.137, C:E.189, C:E.189, C:E.201, C:F.204, C:F.204, C:H.250, C:R.321, C:R.340, J:Y.56, J:F.57, J:D.58
- Salt bridges: C:H.252, C:H.252, C:H.252, C:R.321, C:R.326, C:R.326, C:R.336, C:R.336
- pi-Stacking: C:F.206, C:F.206
- pi-Cation interactions: C:R.336
ATP.27: 20 residues within 4Å:- Chain D: F.133, G.135, E.137, E.189, E.201, D.203, F.204, K.205, F.206, H.252, Q.253, S.254, R.321, R.326, K.333, G.334, T.335, R.336, E.338
- Ligands: PEG.24
28 PLIP interactions:27 interactions with chain D, 1 interactions with chain F- Hydrogen bonds: D:E.189, D:F.206, D:H.250, D:S.254, D:S.254, D:R.321, D:R.336
- Water bridges: D:E.201, D:E.201, D:D.203, D:D.203, D:F.204, D:F.204, D:T.335, D:R.340, D:R.340, F:F.57
- Salt bridges: D:H.252, D:H.252, D:H.252, D:R.321, D:R.326, D:R.326, D:R.336, D:R.336
- pi-Stacking: D:F.206, D:F.206
- pi-Cation interactions: D:R.336
ATP.32: 20 residues within 4Å:- Chain E: F.133, G.135, E.137, E.189, E.201, D.203, F.204, K.205, F.206, H.250, H.252, Q.253, S.254, R.321, R.326, K.333, T.335, R.336, E.338
- Ligands: MG.30
26 PLIP interactions:26 interactions with chain E- Hydrogen bonds: E:E.189, E:E.201, E:F.206, E:S.254, E:S.254, E:R.321, E:R.336
- Water bridges: E:P.136, E:E.137, E:E.201, E:F.204, E:R.321, E:T.335, E:R.336, E:R.336, E:R.340
- Salt bridges: E:H.252, E:H.252, E:H.252, E:R.321, E:R.326, E:R.326, E:R.336
- pi-Stacking: E:F.206, E:F.206
- pi-Cation interactions: E:R.336
ATP.38: 19 residues within 4Å:- Chain F: F.133, G.135, E.137, E.189, E.201, D.203, F.204, K.205, F.206, H.250, H.252, S.254, R.321, R.326, K.333, G.334, T.335, R.336, E.338
31 PLIP interactions:30 interactions with chain F, 1 interactions with chain B- Hydrogen bonds: F:E.137, F:E.189, F:E.201, F:F.206, F:H.250, F:S.254, F:K.333, F:R.336
- Water bridges: F:P.136, F:E.201, F:D.203, F:D.203, F:F.204, F:R.321, F:R.321, F:R.321, F:A.329, F:T.335, F:R.336, B:Y.56
- Salt bridges: F:H.252, F:H.252, F:H.252, F:R.321, F:R.326, F:R.326, F:R.336, F:R.336
- pi-Stacking: F:F.206, F:F.206
- pi-Cation interactions: F:R.336
ATP.46: 19 residues within 4Å:- Chain G: F.133, G.135, E.137, E.189, E.201, D.203, F.204, K.205, F.206, H.250, H.252, Q.253, S.254, R.321, R.326, K.333, T.335, R.336, E.338
22 PLIP interactions:22 interactions with chain G- Hydrogen bonds: G:E.189, G:F.206, G:S.254, G:S.254, G:R.336
- Water bridges: G:P.136, G:F.204, G:R.321, G:R.326, G:T.335, G:R.340
- Salt bridges: G:H.252, G:H.252, G:H.252, G:R.321, G:R.326, G:R.326, G:R.336, G:R.336
- pi-Stacking: G:F.206, G:F.206
- pi-Cation interactions: G:R.336
ATP.49: 20 residues within 4Å:- Chain H: F.133, G.135, E.137, E.189, E.201, D.203, F.204, K.205, F.206, H.250, H.252, Q.253, S.254, R.321, R.326, K.333, G.334, T.335, R.336, E.338
27 PLIP interactions:26 interactions with chain H, 1 interactions with chain G- Hydrogen bonds: H:E.189, H:F.206, H:S.254, H:S.254, H:R.321, H:R.336
- Water bridges: H:P.136, H:H.192, H:E.201, H:E.201, H:E.201, H:F.204, H:H.250, H:R.321, H:R.326, H:R.336, H:R.340, G:F.57
- Salt bridges: H:H.252, H:H.252, H:R.321, H:R.326, H:R.326, H:R.336
- pi-Stacking: H:F.206, H:F.206
- pi-Cation interactions: H:R.336
ATP.53: 20 residues within 4Å:- Chain I: F.133, G.135, E.137, E.189, E.201, D.203, F.204, K.205, F.206, H.250, H.252, Q.253, S.254, R.321, R.326, K.333, G.334, T.335, R.336, E.338
25 PLIP interactions:25 interactions with chain I- Hydrogen bonds: I:E.189, I:E.201, I:F.206, I:S.254, I:S.254, I:R.321
- Water bridges: I:E.137, I:E.201, I:D.203, I:F.204, I:H.250, I:R.321, I:R.326, I:T.335, I:R.340
- Salt bridges: I:H.252, I:H.252, I:H.252, I:R.321, I:R.326, I:R.326, I:R.336, I:R.336
- pi-Stacking: I:F.206, I:F.206
ATP.59: 19 residues within 4Å:- Chain J: F.133, G.135, E.137, E.189, E.201, D.203, F.204, K.205, F.206, H.250, H.252, Q.253, S.254, R.321, R.326, K.333, T.335, R.336, E.338
23 PLIP interactions:23 interactions with chain J- Hydrogen bonds: J:E.137, J:E.189, J:E.201, J:F.206, J:H.250, J:S.254, J:S.254
- Water bridges: J:P.136, J:F.204, J:R.321, J:R.321, J:T.335, J:R.340
- Salt bridges: J:H.252, J:H.252, J:H.252, J:R.321, J:R.326, J:R.326, J:R.336
- pi-Stacking: J:F.206, J:F.206
- pi-Cation interactions: J:R.336
ATP.63: 21 residues within 4Å:- Chain K: F.133, G.135, E.137, E.189, E.201, D.203, F.204, K.205, F.206, H.250, H.252, Q.253, S.254, R.321, R.326, K.333, G.334, T.335, R.336, E.338
- Ligands: MG.61
26 PLIP interactions:26 interactions with chain K- Hydrogen bonds: K:E.189, K:F.206, K:S.254, K:S.254, K:R.336
- Water bridges: K:E.137, K:H.250, K:H.250, K:R.321, K:R.321, K:R.321, K:A.329, K:T.335, K:R.336, K:R.340
- Salt bridges: K:H.252, K:H.252, K:H.252, K:R.321, K:R.326, K:R.326, K:R.336, K:R.336
- pi-Stacking: K:F.206, K:F.206
- pi-Cation interactions: K:R.336
ATP.68: 19 residues within 4Å:- Chain L: F.133, G.135, E.137, E.189, E.201, D.203, F.204, K.205, F.206, H.250, H.252, Q.253, S.254, R.321, R.326, K.333, T.335, R.336, E.338
27 PLIP interactions:24 interactions with chain L, 3 interactions with chain K- Hydrogen bonds: L:E.189, L:E.201, L:F.206, L:H.250, L:S.254, L:S.254, L:R.336
- Water bridges: L:P.136, L:E.201, L:D.203, L:D.203, L:F.204, L:R.321, L:R.340, K:Y.56, K:F.57, K:D.58
- Salt bridges: L:H.252, L:H.252, L:H.252, L:R.321, L:R.326, L:R.326, L:R.336
- pi-Stacking: L:F.206, L:F.206
- pi-Cation interactions: L:R.336
- 12 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)
AKG.9: 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
13 PLIP interactions:6 interactions with chain L, 7 interactions with chain A- Hydrophobic interactions: L:F.18, L:A.34, A:R.175
- Hydrogen bonds: L:R.20, A:P.171
- Salt bridges: L:R.20, L:R.20, L:R.88, A:R.174, A:R.175
- Water bridges: A:R.174, A:R.174, A:R.174
AKG.16: 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
13 PLIP interactions:7 interactions with chain B, 6 interactions with chain H- Hydrophobic interactions: B:R.175, H:F.18, H:A.34
- Hydrogen bonds: B:S.191, H:R.20
- Water bridges: B:R.174, B:R.174, B:R.174
- Salt bridges: B:R.174, B:R.175, H:R.20, H:R.20, H:R.88
AKG.21: 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
13 PLIP interactions:7 interactions with chain C, 6 interactions with chain J- Hydrophobic interactions: C:R.175, J:F.18, J:A.34
- Hydrogen bonds: C:P.171, J:R.20
- Water bridges: C:R.174, C:R.174, C:R.174
- Salt bridges: C:R.174, C:R.175, J:R.20, J:R.20, J:R.88
AKG.28: 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
12 PLIP interactions:6 interactions with chain F, 6 interactions with chain D- Hydrophobic interactions: F:F.18, F:A.34, D:R.175
- Hydrogen bonds: F:R.20
- Salt bridges: F:R.20, F:R.20, F:R.88, D:R.174, D:R.175
- Water bridges: D:R.174, D:R.174, D:R.174
AKG.31: 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
13 PLIP interactions:6 interactions with chain D, 7 interactions with chain E- Hydrophobic interactions: D:F.18, D:A.34, E:R.175
- Hydrogen bonds: D:R.20, E:P.171
- Salt bridges: D:R.20, D:R.20, D:R.88, E:R.174, E:R.175
- Water bridges: E:R.174, E:R.174, E:R.174
AKG.37: 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
13 PLIP interactions:7 interactions with chain F, 6 interactions with chain B- Hydrophobic interactions: F:R.175, B:F.18, B:A.34
- Hydrogen bonds: F:P.171, B:R.20
- Water bridges: F:R.174, F:R.174, F:R.174
- Salt bridges: F:R.174, F:R.175, B:R.20, B:R.20, B:R.88
AKG.45: 10 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, H.192
13 PLIP interactions:6 interactions with chain E, 7 interactions with chain G- Hydrophobic interactions: E:F.18, E:A.34, G:R.175
- Hydrogen bonds: E:R.20, G:S.191
- Salt bridges: E:R.20, E:R.20, E:R.88, G:R.174, G:R.175
- Water bridges: G:R.174, G:R.174, G:R.174
AKG.48: 9 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
13 PLIP interactions:6 interactions with chain G, 7 interactions with chain H- Hydrophobic interactions: G:F.18, G:A.34, H:R.175
- Hydrogen bonds: G:R.20, H:S.191
- Salt bridges: G:R.20, G:R.20, G:R.88, H:R.174, H:R.175
- Water bridges: H:R.174, H:R.174, H:R.174
AKG.52: 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
11 PLIP interactions:5 interactions with chain C, 6 interactions with chain I- Hydrophobic interactions: C:A.34, I:R.175
- Water bridges: C:A.34, I:R.174, I:R.174
- Salt bridges: C:R.20, C:R.20, C:R.88, I:R.174, I:R.175
- Hydrogen bonds: I:S.191
AKG.58: 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
13 PLIP interactions:6 interactions with chain A, 7 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
- Water bridges: J:R.174, J:R.174, J:R.174
AKG.62: 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
12 PLIP interactions:7 interactions with chain K, 5 interactions with chain I- Hydrophobic interactions: K:R.175, I:F.18, I:A.34
- Hydrogen bonds: K:S.191, I:R.20
- Water bridges: K:R.174, K:R.174, K:R.174
- Salt bridges: K:R.174, K:R.175, I:R.20, I:R.88
AKG.67: 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
13 PLIP interactions:7 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
- Water bridges: L:R.174, L:R.174, L:R.174
- Salt bridges: L:R.174, L:R.175, K:R.20, K:R.20, K:R.88
- 2 x MOE: METHOXY-ETHOXYL(Non-covalent)
MOE.12: 7 residues within 4Å:- Chain B: L.27, P.296, T.297, S.345, K.426
- Chain I: Y.445
- Ligands: EDO.54
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:K.426
MOE.39: 4 residues within 4Å:- Chain C: F.242
- Chain F: S.432, S.436, V.437
4 PLIP interactions:1 interactions with chain C, 3 interactions with chain F- Water bridges: C:F.242, F:S.436
- Hydrogen bonds: F:V.437, F:V.437
- 3 x MG: MAGNESIUM ION(Non-covalent)
MG.14: 4 residues within 4Å:- Chain B: H.192, E.201, D.203
- Ligands: ATP.15
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:H.192, B:D.203, H2O.77
MG.30: 4 residues within 4Å:- Chain E: H.192, E.201, D.203
- Ligands: ATP.32
3 PLIP interactions:1 interactions with chain E, 2 Ligand-Water interactions- Metal complexes: E:D.203, H2O.37, H2O.40
MG.61: 4 residues within 4Å:- Chain K: E.137, E.201, D.203
- Ligands: ATP.63
2 PLIP interactions:1 interactions with chain K, 1 Ligand-Water interactions- Metal complexes: K:D.203, H2O.87
- 2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
PG4.22: 6 residues within 4Å:- Chain D: D.439, W.440, T.443, A.444
- Chain J: S.432
- Ligands: PEG.55
2 PLIP interactions:1 interactions with chain J, 1 interactions with chain D- Hydrogen bonds: J:S.432, D:D.439
PG4.26: 17 residues within 4Å:- Chain D: V.298, Y.301, K.302, A.395, N.396, L.397, W.430, F.433
- Chain J: V.298, Y.301, K.302, A.395, N.396, L.397, W.430, F.433, R.434
4 PLIP interactions:2 interactions with chain J, 2 interactions with chain D- Hydrogen bonds: J:L.397, D:L.397
- Water bridges: J:N.396, D:N.396
- 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
AB
BC
CD
DE
EF
FG
GH
HI
IJ
JK
KL
L
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.15 Å
- Oligo State
- homo-12-mer
- Ligands
- 26 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 10 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 1 x GOL: GLYCEROL(Non-functional Binders)
- 12 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
- 12 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)
- 2 x MOE: METHOXY-ETHOXYL(Non-covalent)
- 3 x MG: MAGNESIUM ION(Non-covalent)
- 2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
- 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
AB
BC
CD
DE
EF
FG
GH
HI
IJ
JK
KL
L