SMTL ID : 6oz5.1

Escherichia coli tRNA synthetase in complex with compound 3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-mer

Ligands

2 x VB3: 2-({[(2S)-1-cyclohexylpropan-2-yl]amino}methyl)phenol(Non-covalent)

VB3.1: 14 residues within 4Å: Chain A: L.148, Q.174, S.176, Q.179, I.180, E.215, F.253, F.255, G.276, C.277, V.284, A.299, F.300, G.301 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.148, A:Q.174, A:Q.179, A:I.180, A:F.255, A:F.255, A:V.284, A:A.299 Hydrogen bonds: A:E.215 pi-Stacking: A:F.253, A:F.255 VB3.7: 15 residues within 4Å: Chain C: L.148, Q.174, Q.179, I.180, M.183, E.215, F.253, F.255, T.256, G.276, C.277, V.284, A.299, F.300, G.301 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:L.148, C:L.148, C:Q.174, C:Q.179, C:I.180, C:F.255, C:T.256, C:V.284 Hydrogen bonds: C:E.215 Water bridges: C:Q.179 pi-Stacking: C:F.253, C:F.255

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: E.257 Chain B: E.463 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: B:E.463, A:E.257, H2O.1, H2O.2, H2O.2, H2O.2 MG.8: 3 residues within 4Å: Chain C: E.257 Chain D: D.460, E.463 6 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: D:E.463, C:E.257, H2O.6, H2O.7, H2O.8, H2O.8

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

EDO.3: 4 residues within 4Å: Chain A: I.106 Chain B: R.568, R.600, D.616 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.600, B:D.616 EDO.4: 6 residues within 4Å: Chain B: P.366, P.401, K.402, S.450, R.452, F.453 No protein-ligand interaction detected (PLIP) EDO.6: 6 residues within 4Å: Chain B: H.265, I.304, M.313, G.314, G.315, E.334 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.315 EDO.9: 6 residues within 4Å: Chain D: F.122, I.127, S.128, K.235, E.236, R.239 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.128, D:S.128, D:K.235, D:E.236 EDO.10: 6 residues within 4Å: Chain D: P.366, P.401, S.450, R.452, F.453, E.456 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.456 Water bridges: D:P.401, D:R.403 EDO.11: 6 residues within 4Å: Chain D: H.265, I.304, M.313, G.314, G.315, E.334 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.315, D:E.334 EDO.12: 7 residues within 4Å: Chain D: W.7, E.10, W.11, P.190, K.237, Y.255, E.259 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.10, D:K.237, D:Y.255, D:E.259, D:E.259 EDO.13: 3 residues within 4Å: Chain A: K.332 Chain B: N.503 Chain D: R.497 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: D:R.497, B:N.503, A:K.332

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

PEG.5: 7 residues within 4Å: Chain B: M.1, I.160, V.162, L.170, D.355, H.358, R.359 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:M.1, B:V.162, B:V.162, B:D.355, B:D.355, B:R.359

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

PGE.14: 9 residues within 4Å: Chain D: M.1, I.160, S.161, V.162, L.170, H.353, D.355, H.358, R.359 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:M.1, D:V.162, D:R.359

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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