SMTL ID : 3o6x.1

Crystal Structure of the type III Glutamine Synthetase from Bacteroides fragilis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-hexamer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: E.215, H.342, E.472, R.474 Ligands: P3S.3, ADP.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.215, A:E.215, A:H.342, A:E.472 MG.2: 4 residues within 4Å: Chain A: E.217, E.286, E.293 Ligands: P3S.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.286 MG.8: 5 residues within 4Å: Chain B: E.215, H.342, E.472 Ligands: P3S.10, ADP.11 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.215, B:E.215, B:H.342, B:E.472 MG.9: 5 residues within 4Å: Chain B: E.217, H.284, E.286, E.293 Ligands: P3S.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.217, B:E.286 MG.14: 5 residues within 4Å: Chain C: E.215, H.342, E.472 Ligands: P3S.16, ADP.17 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.215, C:E.215, C:H.342, C:E.472 MG.15: 5 residues within 4Å: Chain C: E.217, H.284, E.286, E.293 Ligands: P3S.16 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.217, C:E.286 MG.20: 5 residues within 4Å: Chain D: E.215, H.342, E.472 Ligands: P3S.22, ADP.23 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.215, D:E.215, D:H.342, D:E.472 MG.21: 5 residues within 4Å: Chain D: E.217, H.284, E.286, E.293 Ligands: P3S.22 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.217, D:E.286 MG.26: 5 residues within 4Å: Chain E: E.215, H.342, E.472 Ligands: P3S.28, ADP.29 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:E.215, E:E.215, E:H.342, E:E.472 MG.27: 5 residues within 4Å: Chain E: E.217, H.284, E.286, E.293 Ligands: P3S.28 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:E.217, E:E.286 MG.32: 5 residues within 4Å: Chain F: E.215, H.342, E.472 Ligands: P3S.34, ADP.35 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:E.215, F:E.215, F:H.342, F:E.472 MG.33: 5 residues within 4Å: Chain F: E.217, H.284, E.286, E.293 Ligands: P3S.34 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:E.217, F:E.286

6 x P3S: L-METHIONINE-S-SULFOXIMINE PHOSPHATE(Non-covalent)

P3S.3: 17 residues within 4Å: Chain A: E.215, E.217, H.284, E.286, V.287, E.293, G.338, S.339, G.340, H.342, R.398, N.402, E.403, R.460 Ligands: MG.1, MG.2, ADP.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:E.403 Hydrogen bonds: A:E.215, A:E.217, A:G.338, A:R.460 Salt bridges: A:H.342, A:R.398 P3S.10: 15 residues within 4Å: Chain B: E.215, E.217, E.286, V.287, E.293, N.337, G.338, S.339, G.340, H.342, R.398, E.403 Ligands: MG.8, MG.9, ADP.11 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.215, B:E.217, B:N.337, B:G.338 Salt bridges: B:H.342, B:R.398 P3S.16: 15 residues within 4Å: Chain C: E.215, E.217, E.286, V.287, E.293, N.337, G.338, S.339, G.340, H.342, R.398, E.403 Ligands: MG.14, MG.15, ADP.17 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.215, C:E.217, C:N.337, C:G.338 Salt bridges: C:H.342, C:R.398 P3S.22: 15 residues within 4Å: Chain D: E.215, E.217, E.286, V.287, E.293, N.337, G.338, S.339, G.340, H.342, R.398, E.403 Ligands: MG.20, MG.21, ADP.23 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:E.215, D:E.217, D:N.337, D:G.338 Salt bridges: D:H.342, D:R.398 P3S.28: 15 residues within 4Å: Chain E: E.215, E.217, E.286, V.287, E.293, N.337, G.338, S.339, G.340, H.342, R.398, E.403 Ligands: MG.26, MG.27, ADP.29 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:E.215, E:E.217, E:N.337, E:G.338 Salt bridges: E:H.342, E:R.398 P3S.34: 15 residues within 4Å: Chain F: E.215, E.217, E.286, V.287, E.293, N.337, G.338, S.339, G.340, H.342, R.398, E.403 Ligands: MG.32, MG.33, ADP.35 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:E.215, F:E.217, F:N.337, F:G.338 Salt bridges: F:H.342, F:R.398

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.4: 17 residues within 4Å: Chain A: G.213, W.214, E.215, E.293, A.295, P.296, F.298, H.342, N.344, S.346, N.354, N.469, R.470, E.472, R.474 Ligands: MG.1, P3S.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:G.213, A:W.214, A:E.293, A:P.296, A:F.298, A:N.344, A:S.346, A:S.346, A:N.354, A:R.470, A:R.470, A:E.472, A:R.474 pi-Stacking: A:F.298 pi-Cation interactions: A:R.470 ADP.11: 14 residues within 4Å: Chain B: G.213, W.214, E.215, E.293, A.295, P.296, F.298, N.344, S.346, N.469, R.470, E.472 Ligands: MG.8, P3S.10 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.213, B:W.214, B:E.293, B:P.296, B:F.298, B:N.344, B:S.346, B:S.346, B:N.354, B:R.470, B:R.470 pi-Stacking: B:F.298 pi-Cation interactions: B:R.470 ADP.17: 14 residues within 4Å: Chain C: G.213, W.214, E.215, E.293, A.295, P.296, F.298, N.344, S.346, N.469, R.470, E.472 Ligands: MG.14, P3S.16 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:G.213, C:W.214, C:E.293, C:P.296, C:F.298, C:N.344, C:S.346, C:S.346, C:N.354, C:R.470, C:R.470 pi-Stacking: C:F.298 pi-Cation interactions: C:R.470 ADP.23: 14 residues within 4Å: Chain D: G.213, W.214, E.215, E.293, A.295, P.296, F.298, N.344, S.346, N.469, R.470, E.472 Ligands: MG.20, P3S.22 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:G.213, D:W.214, D:E.293, D:P.296, D:F.298, D:N.344, D:S.346, D:S.346, D:N.354, D:R.470, D:R.470 pi-Stacking: D:F.298 pi-Cation interactions: D:R.470 ADP.29: 14 residues within 4Å: Chain E: G.213, W.214, E.215, E.293, A.295, P.296, F.298, N.344, S.346, N.469, R.470, E.472 Ligands: MG.26, P3S.28 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:G.213, E:W.214, E:E.293, E:P.296, E:F.298, E:N.344, E:S.346, E:S.346, E:N.354, E:R.470, E:R.470 pi-Stacking: E:F.298 pi-Cation interactions: E:R.470 ADP.35: 14 residues within 4Å: Chain F: G.213, W.214, E.215, E.293, A.295, P.296, F.298, N.344, S.346, N.469, R.470, E.472 Ligands: MG.32, P3S.34 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:G.213, F:W.214, F:E.293, F:P.296, F:F.298, F:N.344, F:S.346, F:S.346, F:N.354, F:R.470, F:R.470 pi-Stacking: F:F.298 pi-Cation interactions: F:R.470

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 4 residues within 4Å: Chain A: K.721, R.723 Chain B: N.613, H.614 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: Q.601, R.605, R.674, N.678 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: N.613, H.614 Chain F: K.721, R.723 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: K.721, R.723 Chain C: N.613, H.614 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain B: Q.601, R.605, R.674, N.678 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain C: K.721, R.723 Chain D: N.613, H.614 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain C: Q.601, R.605, R.674, N.678 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain D: K.721, R.723 Chain E: N.613, H.614 Ligand excluded by PLIP CL.25: 4 residues within 4Å: Chain D: Q.601, R.605, R.674, N.678 Ligand excluded by PLIP CL.30: 4 residues within 4Å: Chain E: K.721, R.723 Chain F: N.613, H.614 Ligand excluded by PLIP CL.31: 4 residues within 4Å: Chain E: Q.601, R.605, R.674, N.678 Ligand excluded by PLIP CL.36: 4 residues within 4Å: Chain F: Q.601, R.605, R.674, N.678 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

van Rooyen, J.M. et al., Crystal Structure of Type III Glutamine Synthetase: Surprising Reversal of the Inter-Ring Interface. Structure (2011)

Release Date

2011-03-09

Peptides

Glutamine synthetase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Glutamine synthetase