SMTL ID : 9lot.1

Crystal structure of Escherichia coli trptophanyl-tRNA synthetase in complex with N-piperidine ibrutinib

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-dimer

Ligands

1 x 01: 3-(4-phenoxyphenyl)-1-piperidin-4-yl-pyrazolo[3,4-d]pyrimidin-4-amine

01.1: 14 residues within 4Å: Chain A: F.7, G.9, Q.11, V.42, H.45, T.48, L.125, Y.128, M.132, D.135, I.136, D.149, Q.150, H.153 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.7, A:F.7, A:Q.11, A:V.42, A:H.45, A:Y.128, A:I.136 Hydrogen bonds: A:H.45, A:H.45 Water bridges: A:Q.11 pi-Stacking: A:H.45, A:Y.128, A:Y.128

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

SO4.2: 3 residues within 4Å: Chain A: N.20, S.197, K.198 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.20, A:K.198 SO4.3: 3 residues within 4Å: Chain A: M.269, Y.270, G.271 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.271 Water bridges: A:Y.270, A:H.272 SO4.6: 5 residues within 4Å: Chain B: K.113, K.195, S.197, K.198, S.199 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:K.198, B:S.199 Water bridges: B:K.195, B:K.195, B:K.195, B:K.195, B:K.198, 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: 14 residues within 4Å: Chain A: A.89, G.92, W.93, N.96, D.127, V.130, L.131 Chain B: A.89, G.92, W.93, N.96, D.127, V.130, L.131 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.93, B: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 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:F.7, B:F.7, B:V.42, B:I.136, B:V.144, B:V.146 Hydrogen bonds: B:Q.11, B:N.20, B:G.23, B:Y.128, B:Y.128, B:D.135, B:D.135, B:G.147, B:D.149, B:V.186, B:K.195, B:M.196, B:M.196 Water bridges: B:P.145, B:E.148, B:E.148, B:Q.150, B:K.198 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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