SMTL ID : 9lpd.1

Crystal structure of Escherichia coli trptophanyl-tRNA synthetase in complex with tirabrutinib

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

1 x 01: Tirabrutinib

01.1: 17 residues within 4Å: Chain A: F.7, G.9, Q.11, V.42, H.45, T.48, M.107, T.108, L.125, Y.128, M.132, D.135, I.136, D.149, Q.150, Q.152, H.153 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.7, A:F.7, A:Q.11, A:V.42, A:H.45, A:M.107, A:Y.128, A:I.136 Hydrogen bonds: A:H.45, A:H.45, A:Q.150 pi-Stacking: A:H.45, A:Y.128, A:Y.128

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain A: M.269, G.271 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.271 Water bridges: A:Y.270, A:Y.270 SO4.3: 3 residues within 4Å: Chain A: N.20, S.197, K.198 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.20, A:K.198, A:S.199 SO4.6: 5 residues within 4Å: Chain B: K.113, K.195, S.197, K.198, S.199 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.198, B:S.199 Salt bridges: B:K.113, B:K.195, B:K.198

1 x CLW: CHLORZOXAZONE(Non-covalent)

CLW.4: 13 residues within 4Å: Chain A: A.89, G.92, W.93, N.96, D.127, L.131 Chain B: A.89, G.92, W.93, N.96, D.127, V.130, L.131 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.93, A:W.93 Hydrogen bonds: B:N.96, B:D.127, A:N.96 pi-Stacking: A:W.93

1 x TYM: TRYPTOPHANYL-5'AMP(Non-covalent)

TYM.5: 27 residues within 4Å: Chain B: F.7, S.8, G.9, A.10, Q.11, G.19, N.20, G.23, A.24, V.42, H.45, Y.128, M.132, D.135, I.136, V.144, V.146, G.147, D.149, Q.150, G.183, A.184, R.185, V.186, K.195, M.196, K.198 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:F.7, B:V.42, B:I.136, B:V.144, B:V.146 Hydrogen bonds: B:Q.11, B:N.20, B:Y.128, B:Y.128, B:D.135, B:D.135, B:G.147, B:D.149, B:V.186, B:V.186, B:K.195, B:M.196 Water bridges: B:E.148, B:D.149 Salt bridges: B:K.198

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peng, X. et al., The lineage-specific tRNA recognition mechanism of bacterial trptophanyl-tRNA synthetase and its implications for inhibitor discover. To Be Published

Release Date

2025-05-07

Peptides

Tryptophan--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tryptophan--tRNA ligase

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