SMTL ID : 9dsx.1

Crystal structure of the complex of M. tuberculosis PheRS with cognate precursor tRNA and fragment DDD00107555

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-2-2-mer

Ligands

2 x 01: ethyl (2R)-2-(3-oxo-2,3-dihydro-4H-1,4-benzoxazin-4-yl)propanoate

01.1: 13 residues within 4Å: Chain A: H.176, S.178, R.202, Q.216, E.218, F.256, F.258, G.283, C.284, A.306, F.307, G.308, G.310 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.256 Hydrogen bonds: A:R.202, A:Q.216, A:G.283 Salt bridges: A:R.202 pi-Stacking: A:F.256, A:F.258 01.25: 10 residues within 4Å: Chain D: H.176, S.178, Q.216, E.218, F.256, F.258, G.283, C.284, F.307, G.308 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.256 Hydrogen bonds: D:Q.216, D:G.283 pi-Stacking: D:F.256, D:F.258

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

MG.2: 3 residues within 4Å: Chain A: E.260 Chain B: D.176, E.480 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: B:E.480, A:E.260, H2O.2, H2O.2, H2O.9, H2O.11 MG.19: 2 residues within 4Å: Chain C: G.42, G.43 No protein-ligand interaction detected (PLIP) MG.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.21: 1 residues within 4Å: Chain C: U.12 No protein-ligand interaction detected (PLIP) MG.26: 3 residues within 4Å: Chain D: E.260 Chain E: D.176, E.480 6 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: D:E.260, E:E.480, H2O.34, H2O.39, H2O.41, H2O.42

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

ACT.3: 4 residues within 4Å: Chain A: H.254, E.264, E.280 Chain B: E.40 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.264 Salt bridges: A:H.254 ACT.14: 3 residues within 4Å: Chain B: R.82, Q.83, Y.84 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.84 ACT.15: 4 residues within 4Å: Chain B: D.417, W.418, S.419, S.467 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.418 ACT.16: 4 residues within 4Å: Chain B: I.45, L.47, N.136, L.137 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.136 Water bridges: B:N.136 ACT.30: 5 residues within 4Å: Chain E: A.381, D.416, D.417, W.418, S.419 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.417, E:D.417, E:W.418 ACT.31: 4 residues within 4Å: Chain E: Q.440, G.441, T.442, R.445 3 PLIP interactions: 3 interactions with chain E Water bridges: E:Q.440, E:R.445 Salt bridges: E:R.445 ACT.32: 5 residues within 4Å: Chain E: G.329, M.331, G.332, E.348, W.352 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:W.352 Hydrogen bonds: E:G.329 Water bridges: E:W.352, E:Y.374 Salt bridges: E:H.279

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 1 residues within 4Å: Chain E: A.657 1 PLIP interactions: 1 interactions with chain E Water bridges: E:E.655 NA.33: 2 residues within 4Å: Chain E: R.793, G.830 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.793, E:G.830 Water bridges: E:A.755

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 13 residues within 4Å: Chain B: H.279, H.281, A.326, I.327, G.328, G.329, V.330, M.331, G.332, E.348, W.352, A.370, Y.374 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.279, B:G.329, B:W.352 Water bridges: B:E.348 GOL.6: 6 residues within 4Å: Chain A: H.153 Chain B: P.175, D.176, T.377, D.471, R.473 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.377, B:R.473, B:R.473 GOL.7: 4 residues within 4Å: Chain B: V.264, H.279, L.304, E.337 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.279, B:E.337, B:E.337 Water bridges: B:H.279, B:A.280 GOL.8: 4 residues within 4Å: Chain B: D.431, G.435, V.436, A.437 No protein-ligand interaction detected (PLIP) GOL.17: 3 residues within 4Å: Chain A: G.225, L.226 Chain B: R.432 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.226, A:S.303 GOL.22: 5 residues within 4Å: Chain B: V.578, V.581, S.582, G.714 Chain C: G.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.578 Water bridges: B:V.581 GOL.23: 7 residues within 4Å: Chain B: A.500, G.501, R.502 Chain D: M.127, A.237, R.240 Chain E: L.495 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.240 GOL.28: 5 residues within 4Å: Chain D: V.105, P.106 Chain E: S.521, G.522, R.642 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.521, E:R.642 GOL.29: 5 residues within 4Å: Chain E: D.431, R.432, G.435, V.436, A.437 1 PLIP interactions: 1 interactions with chain E Water bridges: E:G.435 GOL.34: 2 residues within 4Å: Chain E: V.264, N.268 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:N.268, E:S.368, E:S.368 Water bridges: E:T.267, E:E.369 GOL.35: 5 residues within 4Å: Chain F: C.30, G.31, C.32, A.38, A.39 No protein-ligand interaction detected (PLIP)

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.9: 5 residues within 4Å: Chain B: L.196, D.197, F.198, A.448, Q.449 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.197, B:F.198 DMS.11: 6 residues within 4Å: Chain A: V.105 Chain B: L.520, S.521 Chain D: V.105 Chain E: L.520, S.521 No protein-ligand interaction detected (PLIP) DMS.24: 5 residues within 4Å: Chain B: A.756, D.757 Chain D: E.94, G.95, I.96 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:D.757

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

PGE.10: 6 residues within 4Å: Chain B: E.14, V.15, V.18, P.201, R.206 Ligands: EPE.13 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.206 Water bridges: B:V.15, B:Y.269, B:Y.269, B:R.389, B:R.389 PGE.18: 8 residues within 4Å: Chain A: L.100 Chain B: G.646, P.647, W.648, G.649 Chain E: F.781, D.782, V.783 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:V.783 Water bridges: B:G.646 PGE.27: 9 residues within 4Å: Chain D: I.114, A.117, E.118, A.121, L.131, I.197 Chain E: L.504, Q.508, R.512 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Q.508, E:R.512 Water bridges: E:R.511

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.12: 8 residues within 4Å: Chain B: P.49, V.50, D.51, G.52, D.157, A.159, L.164, D.165 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.50, B:G.52, B:G.52 Salt bridges: B:D.157, B:D.157 EPE.13: 6 residues within 4Å: Chain B: E.14, W.247, R.251, R.389, L.393 Ligands: PGE.10 8 PLIP interactions: 8 interactions with chain B Water bridges: B:W.247, B:R.251, B:R.251, B:R.389, B:R.389 Salt bridges: B:E.14, B:E.14, B:R.389

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gade, P. et al., Different chemical scaffolds bind to L-phe site in Mycobacterium tuberculosis Phe-tRNA synthetase. Eur.J.Med.Chem. (2025)

Release Date

2025-06-04

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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