SMTL ID : 8t5n.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.178, R.304 Ligands: AMP.12 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.178, H2O.1, H2O.3, H2O.5, H2O.8, H2O.11 MG.2: 1 residues within 4Å: Chain A: E.297 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.297, H2O.4, H2O.4, H2O.8, H2O.15 MG.13: 3 residues within 4Å: Chain B: E.178, R.304 Ligands: AMP.24 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:E.178, H2O.15, H2O.17, H2O.19, H2O.22, H2O.25 MG.14: 1 residues within 4Å: Chain B: E.297 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.297, H2O.18, H2O.18, H2O.22, H2O.29

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 2 residues within 4Å: Chain A: T.45, S.47 No protein-ligand interaction detected (PLIP) CA.15: 2 residues within 4Å: Chain B: T.45, S.47 No protein-ligand interaction detected (PLIP)

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

EDO.4: 2 residues within 4Å: Chain A: Q.244, R.280 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.280, A:R.280 Water bridges: A:Q.244, A:Q.244, A:R.280 EDO.5: 3 residues within 4Å: Chain A: R.74, D.75, D.76 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.75, A:D.75 EDO.16: 2 residues within 4Å: Chain B: Q.244, R.280 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.280, B:R.280 Water bridges: B:Q.244, B:Q.244, B:R.280 EDO.17: 3 residues within 4Å: Chain B: R.74, D.75, D.76 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.75, B:D.75

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: Q.65, S.69, W.253, D.256, L.257, R.377 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.65, A:S.69, A:W.253, A:R.377, A:R.377 Water bridges: A:Q.65, A:D.256 GOL.18: 6 residues within 4Å: Chain B: Q.65, S.69, W.253, D.256, L.257, R.377 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.65, B:S.69, B:W.253, B:R.377, B:R.377 Water bridges: B:Q.65

10 x IMD: IMIDAZOLE(Non-covalent)

IMD.7: 3 residues within 4Å: Chain A: E.60 Chain B: W.67, I.205 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:W.67, A:E.57 IMD.8: 4 residues within 4Å: Chain A: R.265, W.267, E.285 Ligands: IMD.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.265, A:E.285 pi-Stacking: A:W.267, A:W.267 IMD.9: 3 residues within 4Å: Chain A: M.455, T.456, Q.457 No protein-ligand interaction detected (PLIP) IMD.10: 6 residues within 4Å: Chain A: R.265, E.285, N.293, W.295, G.296 Ligands: IMD.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.265, A:N.293, A:E.297 Water bridges: A:E.285 IMD.11: 3 residues within 4Å: Chain A: S.94, H.96, F.100 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:H.96 IMD.19: 3 residues within 4Å: Chain A: W.67, I.205 Chain B: E.60 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:W.67, B:E.57 IMD.20: 4 residues within 4Å: Chain B: R.265, W.267, E.285 Ligands: IMD.22 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.265, B:E.285 pi-Stacking: B:W.267, B:W.267 IMD.21: 3 residues within 4Å: Chain B: M.455, T.456, Q.457 No protein-ligand interaction detected (PLIP) IMD.22: 6 residues within 4Å: Chain B: R.265, E.285, N.293, W.295, G.296 Ligands: IMD.20 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.265, B:N.293, B:E.297 IMD.23: 3 residues within 4Å: Chain B: S.94, H.96, F.100 1 PLIP interactions: 1 interactions with chain B pi-Stacking: B:H.96

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.12: 16 residues within 4Å: Chain A: R.210, E.212, F.220, R.221, T.222, F.225, Q.227, E.297, L.298, E.299, G.300, A.339, A.340, G.341, R.344 Ligands: MG.1 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:E.212, A:E.212, A:T.222, A:Q.227, A:E.297, A:E.297, A:L.298, A:G.300, A:R.344 Water bridges: A:R.210, A:R.210, A:G.341, A:T.343 Salt bridges: A:R.210 pi-Stacking: A:F.225, A:F.225 pi-Cation interactions: A:R.344, A:R.344 AMP.24: 16 residues within 4Å: Chain B: R.210, E.212, F.220, R.221, T.222, F.225, Q.227, E.297, L.298, E.299, G.300, A.339, A.340, G.341, R.344 Ligands: MG.13 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:E.178, B:E.178, B:E.212, B:T.222, B:Q.227, B:E.297, B:L.298, B:G.300, B:R.344 Water bridges: B:R.210, B:G.341 Salt bridges: B:R.210 pi-Stacking: B:F.225, B:F.225 pi-Cation interactions: B:R.344, B:R.344

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2023-06-28

Peptides

Glycine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glycine--tRNA ligase

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