SMTL ID : 9drt.1

Crystal structure of the complex of M. tuberculosis PheRS with cognate precursor tRNA and fragment DDD00805735

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

hetero-2-2-mer

Ligands

2 x 01: N-(2-anilinoethyl)methanesulfonamide

01.1: 13 residues within 4Å: Chain A: Q.159, H.176, R.202, Q.216, E.218, F.256, F.258, T.259, G.283, C.284, A.306, F.307, G.308 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.259, A:A.306 Hydrogen bonds: A:Q.159, A:E.218 Water bridges: A:T.175 pi-Stacking: A:F.256, A:F.258 01.21: 11 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, G.310 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:T.259, D:A.306 Hydrogen bonds: D:Q.216, D:G.310 pi-Stacking: D:F.256, D:F.258

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: H.153 Chain B: P.175, D.176, T.377, D.471 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.377 Water bridges: B:G.178, B:P.470, B:R.473 GOL.7: 12 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 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.8: 3 residues within 4Å: Chain B: V.264, N.268, L.304 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.268 GOL.9: 6 residues within 4Å: Chain B: A.202, S.203, N.204, A.381, I.382, A.385 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.381 Water bridges: B:R.184 GOL.10: 6 residues within 4Å: Chain B: D.431, R.432, G.435, V.436, A.437 Ligands: PGE.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.435 GOL.11: 4 residues within 4Å: Chain B: L.196, D.197, F.198, Q.449 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.197, B:D.197, B:F.198 Water bridges: B:R.188, B:A.191, B:Q.449 GOL.12: 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.25: 4 residues within 4Å: Chain E: D.431, G.435, V.436, A.437 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.431, E:G.435 GOL.26: 5 residues within 4Å: Chain E: P.175, D.176, P.470, D.471, R.473 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.473 Water bridges: E:P.175, E:D.471, E:D.471 GOL.27: 9 residues within 4Å: Chain E: H.279, A.326, I.327, G.329, V.330, M.331, G.332, E.348, W.352 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:H.279, E:G.329, E:W.352

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

PGE.3: 7 residues within 4Å: Chain A: G.225, L.226, S.227, A.229 Chain B: R.432, G.435 Ligands: GOL.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.227

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

MG.4: 3 residues within 4Å: Chain A: E.260 Chain B: D.176, E.480 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: A:E.260, B:E.480, H2O.1, H2O.3, H2O.7, H2O.8 MG.5: 3 residues within 4Å: Chain A: E.264, E.280 Chain B: E.40 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:E.264, B:E.40, H2O.3 MG.19: 2 residues within 4Å: Chain C: C.11, U.12 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain C: C.30, G.31 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain D: H.254, E.264 Chain E: E.40 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D Metal complexes: E:E.40, D:E.264, D:E.264 MG.24: 4 residues within 4Å: Chain D: E.260 Chain E: D.176, D.477, 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.26, H2O.29, H2O.31, H2O.32 MG.30: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

NA.6: 1 residues within 4Å: Chain E: A.657 1 PLIP interactions: 1 interactions with chain E Water bridges: E:E.655

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 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.14: 6 residues within 4Å: Chain B: E.14, W.247, R.251, R.389, L.393 Ligands: ACT.17 6 PLIP interactions: 6 interactions with chain B Water bridges: B:R.251, B:R.251, B:R.389 Salt bridges: B:E.14, B:E.14, B:R.389

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

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: 5 residues within 4Å: Chain B: V.161, W.246, W.247, R.250 Ligands: EPE.14 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.250 Salt bridges: B:R.250 ACT.23: 3 residues within 4Å: Chain D: P.150, D.152, H.153 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.152 ACT.28: 5 residues within 4Å: Chain E: A.381, D.416, D.417, W.418, S.419 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:D.417, E:D.417, E:W.418 Water bridges: E:S.467 ACT.29: 4 residues within 4Å: Chain E: Q.440, G.441, T.442, R.445 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.445

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

DMS.18: 5 residues within 4Å: Chain A: V.105 Chain B: L.520, S.521 Chain E: L.520, S.521 No protein-ligand interaction detected (PLIP)

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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