SMTL ID : 6p24.1

Escherichia coli tRNA synthetase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

hetero-2-2-mer

Ligands

13 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: E.257 Chain B: E.463 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Metal complexes: B:E.463, A:E.257 MG.2: 6 residues within 4Å: Chain A: I.106, E.107, N.108 Chain B: N.503, D.504 Chain D: K.505 No protein-ligand interaction detected (PLIP) MG.3: 4 residues within 4Å: Chain A: R.249, E.261, E.273 Chain B: E.31 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Metal complexes: B:E.31, A:E.261, A:E.261, A:E.273, A:E.273 MG.4: 3 residues within 4Å: Chain A: G.313, T.315 Chain D: A.697 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain A: K.332 Chain D: L.627, G.629 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:K.332, H2O.12 MG.12: 2 residues within 4Å: Chain A: R.249 Chain B: E.31 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain A: P.282 Chain B: K.412, L.416, E.459 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.459, H2O.1, H2O.2 MG.14: 3 residues within 4Å: Chain B: T.253, N.254, M.264 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.253, H2O.4 MG.15: 2 residues within 4Å: Chain B: H.488 Chain C: S.123 No protein-ligand interaction detected (PLIP) MG.27: 4 residues within 4Å: Chain C: E.261, E.273 Chain D: E.31 Ligands: EDO.32 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:E.31, C:E.273, H2O.11 MG.28: 4 residues within 4Å: Chain C: E.257 Chain D: D.454, D.460, E.463 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Metal complexes: D:E.463, C:E.257 MG.35: 4 residues within 4Å: Chain D: D.33, E.159, I.160, S.161 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.33 MG.36: 2 residues within 4Å: Chain D: N.687, D.691 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain A: K.267, N.268, L.272 Ligand excluded by PLIP

5 x HEZ: HEXANE-1,6-DIOL(Non-covalent)

HEZ.7: 7 residues within 4Å: Chain A: Q.213, F.253, F.255, G.276, F.300, G.301, M.302 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.253 HEZ.37: 9 residues within 4Å: Chain A: I.97, D.98, L.101 Chain D: Y.615, A.720, V.743, R.745, K.754 Ligands: EDO.26 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:I.97, A:D.98, A:L.101, D:V.743, D:K.754 Hydrogen bonds: A:D.98 HEZ.38: 5 residues within 4Å: Chain D: M.27, G.470, Y.471, N.472, N.473 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:N.472 Hydrogen bonds: D:Y.471, D:N.472, D:N.472, D:N.473 HEZ.39: 8 residues within 4Å: Chain D: W.7, E.10, W.11, W.233, K.237, Y.255, E.259, R.375 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:W.11, D:E.259, D:R.375, D:R.375 HEZ.40: 4 residues within 4Å: Chain D: Y.150, L.151, L.232, W.233 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.151 Hydrogen bonds: D:L.232, D:W.233 Water bridges: D:R.240

4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.8: 7 residues within 4Å: Chain A: G.109, G.110, L.111, K.332 Chain B: N.503 Chain D: R.497, L.627 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: A:L.111, A:K.332, A:K.332, B:T.500, D:R.497 TRS.11: 4 residues within 4Å: Chain A: P.102, R.105 Chain D: E.622, L.724 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:E.622, D:K.728, A:R.105 TRS.33: 8 residues within 4Å: Chain C: G.129, T.131, T.182, Q.186, P.189, I.190, R.191, I.192 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.129, C:Q.186, C:Q.186, C:P.189 TRS.41: 4 residues within 4Å: Chain D: I.199, D.200, D.201, K.222 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.201

10 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 7 residues within 4Å: Chain A: P.189, D.220, T.221, Y.295 Chain B: Q.480, A.481 Chain D: Q.480 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.480, A:P.188 PEG.16: 10 residues within 4Å: Chain B: H.265, I.304, A.312, M.313, G.314, G.315, I.316, F.317, G.318, E.334 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.315, B:I.316, B:I.316, B:G.318, B:E.334 PEG.20: 3 residues within 4Å: Chain B: A.554, V.557, L.673 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.673 PEG.21: 6 residues within 4Å: Chain B: P.138, Y.150, L.151, K.152, L.232, W.233 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.233 PEG.22: 5 residues within 4Å: Chain B: Q.189, P.190, E.191, I.192, K.371 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.192 PEG.23: 8 residues within 4Å: Chain B: A.81, M.118, L.119, S.121, E.124, H.131, G.133, I.134 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.131 PEG.30: 7 residues within 4Å: Chain B: R.497, L.627, R.692 Chain C: N.108, G.109, K.332 Chain D: N.503 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.692, C:K.332 Water bridges: C:L.111 PEG.31: 5 residues within 4Å: Chain C: N.149, Y.252, H.281, N.283 Chain D: I.457 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Y.252, C:Y.252, C:N.283 Water bridges: C:H.281, D:D.460, D:D.460, D:D.460 PEG.47: 11 residues within 4Å: Chain D: P.263, M.264, H.265, I.304, A.312, M.313, G.314, G.315, E.334, A.356, Y.360 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.315, D:E.334, D:Y.360 PEG.49: 5 residues within 4Å: Chain D: K.728, V.735, V.736, G.737, V.738 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.728, D:K.728, D:V.738

17 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.10: 5 residues within 4Å: Chain A: F.240, E.242, L.244, V.264, L.310 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain B: D.423, E.439, G.440, K.441, D.442, E.443, W.444 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain B: P.366, P.401, S.450, F.453 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain A: P.102 Chain B: E.603, H.604, W.605 Chain D: N.739, L.740 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain B: W.605, N.606 Ligands: HEZ.37 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain B: Y.615 Chain C: I.97, D.98, L.101 Chain D: W.605 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain C: Y.252, F.253, E.261 Chain D: E.31, T.163 Ligands: MG.27 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain C: R.197 Chain D: L.495, S.572, G.573 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain D: P.366, P.401, S.450, R.452, F.453 Ligand excluded by PLIP EDO.43: 6 residues within 4Å: Chain D: F.122, S.128, L.232, K.235, E.236, R.239 Ligand excluded by PLIP EDO.44: 6 residues within 4Å: Chain D: H.525, S.547, W.549, R.575, F.661, E.683 Ligand excluded by PLIP EDO.45: 7 residues within 4Å: Chain C: E.107, L.325 Chain D: G.506, Q.508, R.566, V.567, R.568 Ligand excluded by PLIP EDO.46: 4 residues within 4Å: Chain D: P.704, N.706, T.768, L.769 Ligand excluded by PLIP EDO.48: 2 residues within 4Å: Chain D: D.291, G.351 Ligand excluded by PLIP EDO.50: 3 residues within 4Å: Chain D: K.235, S.245, I.246 Ligand excluded by PLIP EDO.51: 6 residues within 4Å: Chain D: R.279, A.305, D.306, H.307, N.308, K.309 Ligand excluded by PLIP EDO.52: 6 residues within 4Å: Chain B: F.741, D.742 Chain D: H.604, W.605, N.606, L.607 Ligand excluded by PLIP

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

PGE.17: 9 residues within 4Å: Chain B: M.1, K.2, V.162, L.170, C.241, L.258, D.355, H.358, R.359 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:M.1, B:K.2, B:I.160, B:V.162, B:C.241, B:R.359, B:R.359 PGE.24: 4 residues within 4Å: Chain A: R.326 Chain B: Q.563 Chain D: I.761, Q.763 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baidin, V. et al., Simple Secondary Amines Inhibit Growth of Gram-Negative Bacteria through Highly Selective Binding to Phenylalanyl-tRNA Synthetase. J.Am.Chem.Soc. (2021)

Release Date

2020-11-18

Peptides

Phenylalanine--tRNA ligase alpha subunit: AC
Phenylalanine--tRNA ligase beta subunit: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Phenylalanine--tRNA ligase alpha subunit

Phenylalanine--tRNA ligase beta subunit

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