SMTL ID : 8slg.1

Crystal Structure of Glycine tRNA ligase from Mycobacterium thermoresistibile (glycyl adenylate bound)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

G5A.1: 20 residues within 4Å: Chain A: E.184, R.216, E.218, F.226, R.227, T.228, F.231, Q.233, E.235, Y.283, E.303, L.304, E.305, G.306, R.310, E.343, A.345, A.346, G.347, R.350 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:E.184, A:R.216, A:E.218, A:E.218, A:T.228, A:Q.233, A:E.235, A:Y.283, A:E.303, A:G.306, A:R.310, A:R.350 Water bridges: A:S.281, A:S.281, A:S.281, A:Y.283, A:G.306, A:T.349 Salt bridges: A:R.216 pi-Stacking: A:F.231, A:F.231 pi-Cation interactions: A:R.350, A:R.350 G5A.7: 20 residues within 4Å: Chain B: E.184, R.216, E.218, F.226, R.227, T.228, F.231, Q.233, E.235, Y.283, E.303, L.304, E.305, G.306, R.310, E.343, A.345, A.346, G.347, R.350 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:R.216, B:E.218, B:T.228, B:Q.233, B:E.235, B:E.303, B:E.303, B:G.306, B:R.310 Water bridges: B:R.216, B:S.281, B:Y.283, B:G.306 Salt bridges: B:R.216 pi-Stacking: B:F.231, B:F.231 pi-Cation interactions: B:R.350, B:R.350

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.111, C.114, C.146, C.149 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.111, A:C.114, A:C.146, A:C.149 ZN.8: 4 residues within 4Å: Chain B: C.111, C.114, C.146, C.149 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.111, B:C.114, B:C.146, B:C.149

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: V.75, R.78, V.81 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:V.75, A:R.78, A:V.81, H2O.6, H2O.8 MG.9: 3 residues within 4Å: Chain B: V.75, R.78, V.81 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:V.75, B:R.78, B:V.81, H2O.3, H2O.11

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: K.67, R.68, W.71, T.211 Chain B: V.60, E.64 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.211, B:E.64 Water bridges: A:T.211, A:T.211 GOL.5: 6 residues within 4Å: Chain A: V.60, E.64 Chain B: K.67, R.68, W.71, T.211 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.68, B:T.211, B:T.211 GOL.6: 5 residues within 4Å: Chain B: R.271, Y.273, E.291, D.299, W.301 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.271, B:D.299

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, L. et al., Crystal Structure of Glycine tRNA ligase from Mycobacterium thermoresistibile (glycyl adenylate bound). To be published

Release Date

2023-05-03

Peptides

Glycine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycine--tRNA ligase

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