SMTL ID : 5ekd.1

Human mitochondrial tryptophanyl-tRNA synthetase bound by indolmycin and Mn*ATP.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-dimer

Ligands

2 x 5BX: (5S)-5-[(1R)-1-(1H-indol-3-yl)ethyl]-2-(methylamino)-1,3-oxazol-4(5H)-one(Non-covalent)

5BX.1: 16 residues within 4Å: Chain A: F.21, S.22, G.23, I.24, Q.25, V.57, H.60, T.63, Y.143, Q.147, D.150, I.151, V.159, V.161, Q.165 Ligands: ATP.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.21, A:F.21, A:Q.25, A:V.57, A:I.151, A:V.159, A:V.161 Hydrogen bonds: A:Q.25, A:H.60, A:Y.143, A:D.150, A:Q.165 5BX.5: 15 residues within 4Å: Chain B: F.21, S.22, G.23, I.24, Q.25, V.57, H.60, Y.143, Q.147, D.150, I.151, V.159, V.161, Q.165 Ligands: ATP.6 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.21, B:F.21, B:Q.25, B:V.57, B:I.151, B:V.159, B:V.161 Hydrogen bonds: B:Q.25, B:H.60, B:D.150, B:D.150, B:Q.165

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 23 residues within 4Å: Chain A: G.23, I.24, Q.25, H.31, G.33, N.34, G.37, A.38, V.161, G.162, D.164, Q.165, M.197, K.198, K.199, V.200, K.209, M.210, S.211, K.212, S.213 Ligands: 5BX.1, MN.3 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:Q.25, A:Q.25, A:N.34, A:G.162, A:D.164, A:V.200, A:K.209, A:M.210, A:M.210, A:K.212, A:S.213, A:S.213 Water bridges: A:E.163, A:E.163, A:K.212 Salt bridges: A:H.31, A:K.209, A:K.209, A:K.212, A:K.212, A:K.212 ATP.6: 23 residues within 4Å: Chain B: G.23, I.24, Q.25, H.31, G.33, N.34, G.37, A.38, V.161, G.162, D.164, Q.165, M.197, K.198, K.199, V.200, K.209, M.210, S.211, K.212, S.213 Ligands: 5BX.5, MN.7 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:Q.25, B:Q.25, B:N.34, B:G.162, B:D.164, B:V.200, B:V.200, B:K.209, B:M.210, B:K.212, B:S.213, B:S.213, B:S.213 Water bridges: B:E.163, B:D.164, B:Q.165, B:K.212 Salt bridges: B:H.31, B:K.209, B:K.209, B:K.212, B:K.212, B:K.212

4 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.3: 3 residues within 4Å: Chain A: Q.25, K.209 Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MN.4: 1 residues within 4Å: Chain A: E.295 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.295, H2O.2, H2O.8 MN.7: 3 residues within 4Å: Chain B: Q.25, K.209 Ligands: ATP.6 No protein-ligand interaction detected (PLIP) MN.8: 1 residues within 4Å: Chain B: E.295 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.295, H2O.12, H2O.19

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 12 residues within 4Å: Chain A: T.104, S.107, W.108, S.111, V.145, L.146 Chain B: T.104, S.107, W.108, S.111, V.145, L.146 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.107, A:S.107, B:S.107, B:S.107 GOL.10: 3 residues within 4Å: Chain B: K.326, E.327, Y.330 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williams, T.L. et al., Binding of Mg2+ATP Enhances Inhibition of Human Mitochondrial Tryptophanyl-tRNA Synthetase by Indolmycin. To Be Published

Release Date

2016-11-16

Peptides

Tryptophan--tRNA ligase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tryptophan--tRNA ligase, mitochondrial