SMTL ID : 8u2p.1

Crystal Structure of Glycine--tRNA ligase from Mycobacterium tuberculosis (G5A bound)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

2 x G5A: 5'-O-(glycylsulfamoyl)adenosine(Non-covalent)

G5A.1: 20 residues within 4Å: Chain A: E.178, R.210, E.212, F.220, R.221, T.222, F.225, Q.227, E.229, Y.277, E.297, L.298, E.299, G.300, R.304, E.337, A.339, G.341, R.344 Ligands: MG.8 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:R.210, A:E.212, A:E.212, A:T.222, A:Q.227, A:E.229, A:Y.277, A:E.297, A:E.297, A:G.300, A:R.304, A:R.344, A:R.344 Water bridges: A:R.210, A:R.210, A:S.275, A:S.275, A:S.275, A:Y.277 Salt bridges: A:R.210 pi-Stacking: A:F.225, A:F.225 pi-Cation interactions: A:R.344, A:R.344 G5A.11: 20 residues within 4Å: Chain B: E.178, R.210, E.212, F.220, R.221, T.222, F.225, Q.227, E.229, Y.277, E.297, L.298, E.299, G.300, R.304, E.337, A.339, G.341, R.344 Ligands: MG.18 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:E.178, B:R.210, B:E.212, B:T.222, B:Q.227, B:E.229, B:E.297, B:G.300, B:R.304, B:R.344, B:R.344 Water bridges: B:R.210, B:S.275, B:S.275, B:S.275, B:Y.277, B:Y.277, B:Y.277 Salt bridges: B:R.210 pi-Stacking: B:F.225, B:F.225 pi-Cation interactions: B:R.344, B:R.344

4 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 4 residues within 4Å: Chain A: K.30 Chain B: N.189, T.192, T.193 2 PLIP interactions: 2 interactions with chain B Water bridges: B:A.188, B:T.192 IMD.3: 4 residues within 4Å: Chain A: L.388, D.438, F.439, D.440 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.439, A:D.440 IMD.12: 4 residues within 4Å: Chain A: N.189, T.192, T.193 Chain B: K.30 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.188, A:T.192 IMD.13: 4 residues within 4Å: Chain B: L.388, D.438, F.439, D.440 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.439, B:D.440

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.4: 3 residues within 4Å: Chain A: E.241, W.242, Y.245 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.241 MES.14: 3 residues within 4Å: Chain B: E.241, W.242, Y.245 No protein-ligand interaction detected (PLIP)

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

EDO.5: 6 residues within 4Å: Chain A: G.258, R.373, L.374, D.375, P.376, R.452 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.452, A:D.453 Water bridges: A:L.257 EDO.6: 4 residues within 4Å: Chain A: R.265, W.267, E.285, N.293 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.267 Water bridges: A:E.285 EDO.7: 4 residues within 4Å: Chain A: H.269, D.283, E.297 Ligands: MG.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.283 EDO.15: 6 residues within 4Å: Chain B: G.258, R.373, L.374, D.375, P.376, R.452 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.452, B:D.453 Water bridges: B:L.257 EDO.16: 4 residues within 4Å: Chain B: R.265, W.267, E.285, N.293 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.267 EDO.17: 4 residues within 4Å: Chain B: H.269, D.283, E.297 Ligands: MG.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.283 Water bridges: B:D.283

2 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 3 residues within 4Å: Chain A: E.297 Ligands: G5A.1, EDO.7 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.297, A:E.297, H2O.2, H2O.3, H2O.3 MG.18: 3 residues within 4Å: Chain B: E.297 Ligands: G5A.11, EDO.17 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.297, B:E.297, H2O.7, H2O.8, H2O.8

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

CL.9: 5 residues within 4Å: Chain A: R.31, R.32, R.425 Chain B: T.192, T.193 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: R.74, D.75 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain A: T.192, T.193 Chain B: R.31, R.32, R.425 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain B: R.74, D.75 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seibold, S. et al., Crystal Structure of Glycine--tRNA ligase from Mycobacterium tuberculosis (G5A bound). To be published

Release Date

2023-09-13

Peptides

Glycine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glycine--tRNA ligase

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