SMTL ID : 7kab.1

M. tuberculosis PheRS complex with cognate precursor tRNA and phenylalanine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-mer

Ligands

2 x PHE: PHENYLALANINE(Non-covalent)

PHE.1: 14 residues within 4Å: Chain A: H.175, S.177, Q.180, R.201, Q.215, E.217, F.255, F.257, T.258, G.282, C.283, A.305, F.306, G.307 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:T.258, A:A.305 Hydrogen bonds: A:H.175, A:S.177, A:S.177, A:Q.215 Water bridges: A:S.177, A:S.177 Salt bridges: A:R.201 pi-Stacking: A:F.255, A:F.257 PHE.20: 14 residues within 4Å: Chain D: H.175, S.177, Q.180, R.201, Q.215, E.217, F.255, F.257, T.258, G.282, C.283, A.305, F.306, G.307 10 PLIP interactions: 10 interactions with chain D, Hydrophobic interactions: D:T.258, D:A.305 Hydrogen bonds: D:H.175, D:S.177, D:Q.215 Water bridges: D:S.177, D:S.177 Salt bridges: D:R.201 pi-Stacking: D:F.255, D:F.257

6 x PGR: R-1,2-PROPANEDIOL(Non-covalent)

PGR.2: 5 residues within 4Å: Chain A: D.151, H.152, R.155, G.156 Chain B: R.362 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.151, A:D.151, A:H.152, A:H.152, B:R.362, B:R.362 PGR.9: 5 residues within 4Å: Chain A: R.182, L.185, A.186 Chain B: I.620, D.624 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.185, A:A.186 Hydrogen bonds: A:R.182, B:D.624 PGR.11: 6 residues within 4Å: Chain A: P.105 Chain B: G.522, D.587, A.589, L.641, R.642 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.589 PGR.21: 5 residues within 4Å: Chain D: D.151, H.152, R.155, G.156 Chain E: R.362 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:R.362, E:R.362, D:D.151, D:H.152, D:H.152 PGR.28: 5 residues within 4Å: Chain D: R.182, L.185, A.186 Chain E: I.620, D.624 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:L.185, D:A.186 Hydrogen bonds: D:R.182, E:D.624 PGR.30: 6 residues within 4Å: Chain D: P.105 Chain E: G.522, D.587, A.589, L.641, R.642 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:A.589

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

MG.3: 2 residues within 4Å: Chain A: G.156, Q.158 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:G.156, A:Q.158, H2O.1, H2O.2, H2O.2 MG.7: 4 residues within 4Å: Chain A: E.259 Chain B: D.176, D.477, E.480 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.259, H2O.3, H2O.4, H2O.4, H2O.4 MG.8: 3 residues within 4Å: Chain A: E.263, E.279 Chain B: E.40 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.263, A:E.279, H2O.5 MG.13: 4 residues within 4Å: Chain B: F.747, E.811 Chain C: A.39 Ligands: MG.14 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:F.747, B:E.811 MG.14: 3 residues within 4Å: Chain C: G.27, A.39 Ligands: MG.13 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain C: A.24, G.46 Ligands: MG.16 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain C: A.9, G.23, A.24 Ligands: MG.15 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain C: G.15, U.16 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain C: C.29, C.30, G.43, A.44 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain C: G.10, G.46, G.47 No protein-ligand interaction detected (PLIP) MG.22: 2 residues within 4Å: Chain D: G.156, Q.158 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:G.156, D:Q.158, H2O.7, H2O.7, H2O.7 MG.26: 4 residues within 4Å: Chain D: E.259 Chain E: D.176, D.477, E.480 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:E.259, H2O.9, H2O.9, H2O.9, H2O.10 MG.27: 3 residues within 4Å: Chain D: E.263, E.279 Chain E: E.40 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.263, D:E.279, H2O.11 MG.32: 4 residues within 4Å: Chain E: F.747, E.811 Chain F: A.39 Ligands: MG.33 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:F.747, E:E.811 MG.33: 3 residues within 4Å: Chain F: G.27, A.39 Ligands: MG.32 No protein-ligand interaction detected (PLIP) MG.34: 3 residues within 4Å: Chain F: A.24, G.46 Ligands: MG.35 No protein-ligand interaction detected (PLIP) MG.35: 4 residues within 4Å: Chain F: A.9, G.23, A.24 Ligands: MG.34 No protein-ligand interaction detected (PLIP) MG.36: 2 residues within 4Å: Chain F: G.15, U.16 No protein-ligand interaction detected (PLIP) MG.37: 4 residues within 4Å: Chain F: C.29, C.30, G.43, A.44 No protein-ligand interaction detected (PLIP) MG.38: 3 residues within 4Å: Chain F: G.10, G.46, G.47 No protein-ligand interaction detected (PLIP)

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: A.131, E.132, T.183, A.186, R.187 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.132, A:R.187, A:R.187 GOL.5: 5 residues within 4Å: Chain A: D.203, T.208, H.209, T.210, F.213 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.210 Water bridges: A:R.201, A:D.203 GOL.6: 5 residues within 4Å: Chain A: R.231, T.248, R.249, W.277 Chain B: E.489 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.231 GOL.23: 5 residues within 4Å: Chain D: A.131, E.132, T.183, A.186, R.187 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.132, D:R.187, D:R.187 GOL.24: 5 residues within 4Å: Chain D: D.203, T.208, H.209, T.210, F.213 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.203, D:T.210 Water bridges: D:R.201, D:D.203 GOL.25: 5 residues within 4Å: Chain D: R.231, T.248, R.249, W.277 Chain E: E.489 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.231

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 7 residues within 4Å: Chain A: P.153, A.154, E.157 Chain B: S.2, N.3, P.175, R.376 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.3 Salt bridges: B:R.376 SO4.29: 7 residues within 4Å: Chain D: P.153, A.154, E.157 Chain E: S.2, N.3, P.175, R.376 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:E.157, E:N.3 Salt bridges: E:R.376

2 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.12: 3 residues within 4Å: Chain B: E.489, I.491, P.492 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.491 Water bridges: B:S.493 PGO.31: 3 residues within 4Å: Chain E: E.489, I.491, P.492 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:I.491 Water bridges: E:S.493

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: AD
Phenylalanine--tRNA ligase beta subunit: BE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

B
B

E
B

Phenylalanine--tRNA ligase alpha subunit

Phenylalanine--tRNA ligase beta subunit

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