SMTL ID : 9dtf.1

Crystal structure of the complex of M. tuberculosis PheRS with cognate precursor tRNA and fragment DDD01008876

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

hetero-2-2-mer

Ligands

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

MG.1: 3 residues within 4Å: Chain A: E.260 Chain B: D.176, E.480 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.260, H2O.5, H2O.6, H2O.6, H2O.12 MG.24: 1 residues within 4Å: Chain C: C.30 No protein-ligand interaction detected (PLIP) MG.25: 2 residues within 4Å: Chain C: C.11, U.12 No protein-ligand interaction detected (PLIP) MG.29: 3 residues within 4Å: Chain D: E.260 Chain E: D.176, E.480 6 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: E:E.480, D:E.260, H2O.27, H2O.28, H2O.29, H2O.30

2 x 01: (5S)-7-benzyl-1,3,7-triazaspiro[4.4]nonane-2,4-dione

01.2: 10 residues within 4Å: Chain A: R.202, F.214, Q.216, E.218, F.256, F.258, G.283, C.284, F.307, G.308 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.202, A:Q.216 Water bridges: A:G.310 pi-Stacking: A:F.256, A:F.258 pi-Cation interactions: A:R.202 01.28: 10 residues within 4Å: Chain D: Q.216, E.218, F.256, F.258, T.259, G.283, C.284, A.306, F.307, G.308 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:T.259, D:A.306 Hydrogen bonds: D:Q.216 pi-Stacking: D:F.256, D:F.258

12 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: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:H.254 Hydrogen bonds: B:E.40 ACT.15: 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.16: 4 residues within 4Å: Chain B: A.381, D.417, W.418, S.419 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.381 Hydrogen bonds: B:W.418 Water bridges: B:S.467 ACT.17: 4 residues within 4Å: Chain B: I.45, L.47, N.136, L.137 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.136 ACT.19: 6 residues within 4Å: Chain B: W.540, L.682, H.706, A.708, R.712 Chain D: D.87 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Water bridges: B:R.712 Salt bridges: B:H.706, B:R.712 Hydrogen bonds: D:D.87 ACT.20: 3 residues within 4Å: Chain B: S.205, R.206 Ligands: PGE.10 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.206 ACT.21: 6 residues within 4Å: Chain B: R.664, V.674, T.675, L.676, Q.761 Chain D: T.99 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Q.761 Hydrogen bonds: B:L.676, B:Q.761 Salt bridges: B:R.664 ACT.22: 4 residues within 4Å: Chain B: R.36, A.193, R.484, L.485 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.193 Salt bridges: B:R.36 ACT.32: 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.33: 4 residues within 4Å: Chain E: Q.440, G.441, T.442, R.445 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.442 Water bridges: E:Q.440 Salt bridges: E:R.445 ACT.34: 6 residues within 4Å: Chain E: I.327, G.329, M.331, G.332, E.348, W.352 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:W.352 Salt bridges: E:H.279 ACT.38: 5 residues within 4Å: Chain E: D.176, T.377, P.470, D.471, R.473 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:D.471 Hydrogen bonds: E:T.377 Water bridges: E:G.178 Salt bridges: E:R.473

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

NA.4: 2 residues within 4Å: Chain E: E.655, A.657 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.655 NA.35: 2 residues within 4Å: Chain E: R.793, G.830 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.793, E:G.830

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 11 residues within 4Å: Chain B: H.279, H.281, A.326, I.327, G.328, G.329, M.331, G.332, E.348, W.352, A.370 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 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.279, B:E.337, B:E.337 Water bridges: B:A.280 GOL.8: 4 residues within 4Å: Chain B: D.431, G.435, V.436, A.437 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.435 GOL.11: 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.18: 2 residues within 4Å: Chain A: G.225 Chain B: R.432 No protein-ligand interaction detected (PLIP) GOL.23: 4 residues within 4Å: Chain B: V.578, S.582, G.714 Chain C: G.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.578 Water bridges: B:G.714 GOL.30: 8 residues within 4Å: Chain D: V.105, P.106 Chain E: S.521, G.522, D.587, A.589, L.641, R.642 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.521, E:A.589, E:R.642 GOL.31: 3 residues within 4Å: Chain E: D.431, G.435, A.437 No protein-ligand interaction detected (PLIP) GOL.36: 2 residues within 4Å: Chain E: V.264, N.268 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.268 GOL.39: 5 residues within 4Å: Chain F: C.30, G.31, C.32, A.38, A.39 No protein-ligand interaction detected (PLIP)

4 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.12: 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.26: 6 residues within 4Å: Chain B: A.756, D.757 Chain D: E.94, G.95, I.96, D.97 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:D.757 DMS.37: 7 residues within 4Å: Chain A: I.96, D.97, V.98 Chain E: P.678, A.756, D.757, P.759 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.97

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

PGE.10: 8 residues within 4Å: Chain B: V.18, P.201, R.206, V.207, E.273, R.389 Ligands: EPE.14, ACT.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.14, B:R.206 PGE.27: 9 residues within 4Å: Chain D: I.114, A.117, L.131, E.136, R.174, I.197, G.198, R.199, H.215 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:E.136, D:R.174, D:R.199, E:R.512

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

EPE.13: 8 residues within 4Å: Chain B: P.49, V.50, D.51, G.52, D.157, A.159, L.164, D.165 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.50, B:G.52, B:G.52 Salt bridges: B:D.51, B:D.157, B:D.157 EPE.14: 5 residues within 4Å: Chain B: W.247, R.251, R.389, L.393 Ligands: PGE.10 7 PLIP interactions: 7 interactions with chain B Water bridges: B:W.247, 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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