SMTL ID : 7ka0.1

Crystal structure of the complex of M. tuberculosis PheRS with cognate precursor tRNA and phenylalanine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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:T.176, A:G.282 Salt bridges: A:R.201 pi-Stacking: A:F.255, A:F.257 PHE.22: 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 13 PLIP interactions: 11 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:T.258, D:A.305 Hydrogen bonds: D:H.175, D:S.177, D:Q.215, D:Q.215, F.22 Water bridges: D:T.176, D:G.282, F.22 Salt bridges: D:R.201 pi-Stacking: D:F.255, D:F.257

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 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.3: 6 residues within 4Å: Chain A: D.203, T.208, H.209, T.210, F.213, M.323 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.203, A:D.203, A:T.208, A:T.210 GOL.6: 3 residues within 4Å: Chain A: D.206, A.207, R.324 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.207, A:R.324 GOL.7: 3 residues within 4Å: Chain A: R.249, W.277 Chain B: Q.32 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.249, A:R.249, B:Q.32 GOL.8: 4 residues within 4Å: Chain A: R.231, R.249, I.250 Chain B: E.489 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:E.489, A:R.231, A:R.231, A:I.250, A:I.250 GOL.12: 5 residues within 4Å: Chain A: G.224, L.225, S.302 Chain B: R.432, I.433 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.225, A:S.302, B:R.432 Water bridges: A:S.226, B:R.432 GOL.15: 4 residues within 4Å: Chain B: D.431, R.432, V.436, A.437 No protein-ligand interaction detected (PLIP) GOL.25: 4 residues within 4Å: Chain D: A.131, E.132, T.183, R.187 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.132, D:R.187, D:R.187 GOL.26: 7 residues within 4Å: Chain D: H.209, T.210, F.213, G.309, L.310, E.311, R.312 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.210, D:E.311, D:R.312 GOL.28: 6 residues within 4Å: Chain D: G.224, L.225, S.226 Chain E: R.432, I.433 Ligands: GOL.36 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.432 GOL.30: 3 residues within 4Å: Chain D: D.206, A.207, R.324 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.206, D:A.207, D:R.324, D:R.324 GOL.36: 6 residues within 4Å: Chain E: D.428, D.431, R.432, G.435, V.436 Ligands: GOL.28 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.428, E:G.435 Water bridges: E:G.435

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 3 residues within 4Å: Chain A: L.24, R.82, R.85 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.82, A:R.82 Salt bridges: A:R.82, A:R.85 ACT.27: 2 residues within 4Å: Chain D: R.82, R.85 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:R.82, D:R.85

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 8 residues within 4Å: Chain A: M.126, A.236, R.239, A.240 Chain B: L.495 Chain E: A.500, G.501, R.502 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.239, A:R.239 PGE.18: 7 residues within 4Å: Chain B: A.500, G.501, R.502 Chain D: A.236, R.239, A.240 Chain E: L.495 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.239 Water bridges: D:R.239 PGE.37: 6 residues within 4Å: Chain E: D.624, L.627, P.628, R.629, Q.630, P.631 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.624, E:Q.630

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

MG.9: 5 residues within 4Å: Chain A: E.259 Chain B: D.176, D.471, D.477, E.480 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:E.480, A:E.259, H2O.8, H2O.9, H2O.10 MG.10: 3 residues within 4Å: Chain A: E.259, H.287 Chain B: D.477 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.287, B:D.477, H2O.9 MG.17: 5 residues within 4Å: Chain B: F.747, Q.748, E.811 Chain C: A.38, A.39 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:F.747 MG.19: 2 residues within 4Å: Chain C: G.27, A.39 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain C: A.44, A.45 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain C: U.34, G.35, A.36 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain D: I.95, L.99 No protein-ligand interaction detected (PLIP) MG.31: 3 residues within 4Å: Chain D: E.259 Chain E: D.176, E.480 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:E.259, H2O.20, H2O.20, H2O.25, H2O.25 MG.33: 5 residues within 4Å: Chain E: F.747, Q.748 Chain F: A.38, A.39 Ligands: MG.40 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:F.747, H2O.23 MG.34: 8 residues within 4Å: Chain E: S.751, D.782, S.795, L.796, T.797, R.834 Chain F: G.35, A.36 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:S.795, E:T.797 MG.40: 5 residues within 4Å: Chain E: E.811 Chain F: G.27, A.39, G.40 Ligands: MG.33 No protein-ligand interaction detected (PLIP) MG.41: 1 residues within 4Å: Chain F: G.46 No protein-ligand interaction detected (PLIP)

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

SO4.11: 7 residues within 4Å: Chain A: P.153, E.157 Chain B: S.2, N.3, I.173, P.175, R.376 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.3, A:E.157 Salt bridges: B:R.376 SO4.13: 3 residues within 4Å: Chain A: N.289 Chain B: R.473, Q.474 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.474, A:N.289 Salt bridges: B:R.473 SO4.16: 3 residues within 4Å: Chain B: Y.743, R.807, T.808 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.808, B:T.808 SO4.24: 3 residues within 4Å: Chain D: R.187, E.188 Chain E: R.502 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Salt bridges: E:R.502 Hydrogen bonds: D:E.188 SO4.32: 7 residues within 4Å: Chain D: P.153, E.157 Chain E: S.2, N.3, I.173, P.175, R.376 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.3, E:I.173 Salt bridges: E:R.376 SO4.35: 3 residues within 4Å: Chain D: N.289 Chain E: R.473, Q.474 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:Q.474, D:N.289, D:N.289 Salt bridges: E:R.473 SO4.39: 3 residues within 4Å: Chain E: Y.743, R.807, T.808 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.808, E:T.808

3 x K: POTASSIUM ION(Non-covalent)

K.14: 3 residues within 4Å: Chain B: T.267, N.268, M.278 No protein-ligand interaction detected (PLIP) K.29: 5 residues within 4Å: Chain D: R.155, G.156, Q.158, T.160, Y.162 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:R.155, D:T.160, D:Y.162, H2O.18 K.38: 4 residues within 4Å: Chain E: E.525, I.526, A.592, I.593 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.525

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
D

B
B

E
E

Phenylalanine--tRNA ligase alpha subunit

Phenylalanine--tRNA ligase beta subunit

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