SMTL ID : 7k98.1

Preaminoacylation complex of M. tuberculosis PheRS with cognate precursor tRNA and 5'-O-(N-phenylalanyl)sulfamoyl-adenosine (F-AMS)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

hetero-2-2-mer

Ligands

2 x W5Y: 5'-O-(L-phenylalanylsulfamoyl)adenosine(Non-covalent)

W5Y.1: 25 residues within 4Å: Chain A: H.178, S.180, Q.183, R.204, D.206, T.211, H.212, T.213, F.216, Q.218, E.220, F.258, F.260, T.261, E.282, W.283, G.284, G.285, C.286, A.308, F.309, G.310, G.312, R.315 Chain E: A.77 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:T.261, A:A.308 Hydrogen bonds: A:S.180, A:S.180, A:R.204, A:D.206, A:D.206, A:T.213, A:Q.218, A:E.282, A:W.283, A:G.312, A:R.315 Water bridges: A:S.180, A:S.180, A:R.204 Salt bridges: A:R.204 pi-Stacking: A:H.212, A:F.216, A:F.216, A:F.258, A:F.260 W5Y.9: 24 residues within 4Å: Chain C: H.178, S.180, Q.183, R.204, D.206, T.211, H.212, T.213, F.216, Q.218, E.220, F.258, F.260, T.261, W.283, G.284, G.285, C.286, A.308, F.309, G.310, G.312, R.315 Chain F: A.77 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:T.261, C:A.308 Hydrogen bonds: C:S.180, C:S.180, C:R.204, C:D.206, C:T.213, C:Q.218, C:E.282, C:G.312, C:R.315 Water bridges: C:S.180, C:S.180, C:R.204, C:G.284 Salt bridges: C:R.204 pi-Stacking: C:F.216, C:F.216, C:F.258, C:F.260

13 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 1 residues within 4Å: Chain A: D.206 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.206, H2O.1, H2O.1, H2O.23, H2O.23, H2O.24 MG.3: 5 residues within 4Å: Chain A: E.262 Chain B: D.181, R.182, D.476, E.485 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: B:E.485, A:E.262, H2O.1, H2O.2, H2O.4, H2O.6 MG.4: 1 residues within 4Å: Chain A: E.207 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain A: H.256, E.266 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.256, H2O.1, H2O.24, H2O.24 MG.6: 3 residues within 4Å: Chain B: E.816 Chain F: G.27, A.39 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.816, H2O.5, H2O.25 MG.10: 3 residues within 4Å: Chain C: D.206 Chain F: C.76, A.77 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:D.206, H2O.13, H2O.14, H2O.25, H2O.25, H2O.25 MG.11: 3 residues within 4Å: Chain C: E.262 Chain D: D.181, E.485 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: C:E.262, D:E.485, H2O.16, H2O.17, H2O.18, H2O.19 MG.12: 1 residues within 4Å: Chain C: H.256 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.256, H2O.13, H2O.15, H2O.25 MG.15: 2 residues within 4Å: Chain E: U.8, A.9 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain D: E.816 Chain E: G.27, A.39 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.816, H2O.17, H2O.23 MG.18: 2 residues within 4Å: Chain F: U.8, A.9 No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Chain C: E.207 No protein-ligand interaction detected (PLIP) MG.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

CL.7: 3 residues within 4Å: Chain B: V.758, G.795, R.798 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain D: V.758, I.794, G.795, R.798 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 2 residues within 4Å: Chain B: E.19, W.252 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.19 GOL.14: 1 residues within 4Å: Chain D: W.252 No protein-ligand interaction detected (PLIP) GOL.17: 3 residues within 4Å: Chain E: C.4, A.5, G.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Michalska, K. et al., Mycobacterium tuberculosis Phe-tRNA synthetase: structural insights into tRNA recognition and aminoacylation. Nucleic Acids Res. (2021)

Release Date

2021-05-12

Peptides

Phenylalanine--tRNA ligase alpha subunit: AC
Phenylalanine--tRNA ligase beta subunit: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
D

B
B

D
E

Phenylalanine--tRNA ligase alpha subunit

Phenylalanine--tRNA ligase beta subunit