SMTL ID : 7ev3.1

Crystal structure of Mycobacterium tuberculosis tryptophanyl-tRNA synthetase complexed with Y-10 and ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

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

ATP.1: 24 residues within 4Å: Chain A: G.13, V.14, Q.15, T.17, H.22, G.24, N.25, G.28, A.29, V.152, G.153, D.155, Q.156, T.189, A.190, K.191, I.192, K.201, M.202, S.203, K.204, S.205 Ligands: MG.2, JE3.3 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:Q.15, A:Q.15, A:T.17, A:N.25, A:G.153, A:G.153, A:I.192, A:I.192, A:K.201, A:K.204, A:S.205 Water bridges: A:P.151, A:D.155, A:Q.156, A:K.201 Salt bridges: A:H.22, A:K.201, A:K.201, A:K.204, A:K.204, A:K.204 ATP.4: 24 residues within 4Å: Chain B: G.13, V.14, Q.15, T.17, H.22, G.24, N.25, G.28, A.29, V.152, G.153, D.155, Q.156, T.189, A.190, K.191, I.192, K.201, M.202, S.203, K.204, S.205 Ligands: MG.5, JE3.6 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:Q.15, B:Q.15, B:N.25, B:G.153, B:G.153, B:I.192, B:I.192, B:K.201, B:K.204, B:S.205 Water bridges: B:P.151, B:D.155, B:D.155, B:Q.156, B:K.201 Salt bridges: B:H.22, B:K.201, B:K.201, B:K.204, B:K.204, B:K.204

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

MG.2: 2 residues within 4Å: Ligands: ATP.1, JE3.3 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Ligands: ATP.4, JE3.6 No protein-ligand interaction detected (PLIP)

2 x JE3: (5S)-5-[(1R)-1-(4-fluoranyl-1H-indol-3-yl)ethyl]-2-(methylamino)-1,3-oxazol-4-one(Non-covalent)

JE3.3: 15 residues within 4Å: Chain A: F.11, S.12, G.13, Q.15, V.47, H.50, T.53, Y.134, Q.138, D.141, V.142, V.152, Q.156 Ligands: ATP.1, MG.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.11, A:F.11, A:Q.15, A:Q.138, A:D.141, A:V.142, A:V.152 Hydrogen bonds: A:H.50, A:D.141, A:Q.156 JE3.6: 15 residues within 4Å: Chain B: F.11, S.12, G.13, Q.15, V.47, H.50, T.53, Y.134, Q.138, D.141, V.142, V.152, Q.156 Ligands: ATP.4, MG.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.11, B:F.11, B:Q.15, B:Q.138, B:D.141, B:V.142, B:V.152 Hydrogen bonds: B:H.50, B:D.141, B:D.141, B:Q.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Y. et al., Investigate Natural Product Indolmycin and the Synthetically Improved Analogue Toward Antimycobacterial Agents. Acs Chem.Biol. (2022)

Release Date

2022-02-16

Peptides

Tryptophan--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Tryptophan--tRNA ligase

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