4HWT: Human Threonyl-tRNA synthetase

Crystal structure of human Threonyl-tRNA synthetase bound to a novel inhibitor. Determined by X-ray diffraction at 2.3 Å resolution. Released 18 Sept 2013.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,972
Mol. weight: 97.83 kDa
Ligands: 1B2, ZN
Released: 18 Sept 2013

Explore 4HWT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4HWT contains 42 α-helices and 55 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 20 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	356-362	7
β-strand	366-367	2	1
β-strand	377-378	2	1
α-helix	380-399	20
β-strand	403-404	2	2
β-strand	406	1	3
β-strand	410-412	3	4
α-helix	413-419	7
α-helix	421-424	4
α-helix	426-428	3
β-strand	431-434	4	4
β-strand	437-441	5	4
α-helix	446-454	9
β-strand	459	1	5
α-helix	460-462	3
β-strand	465-469	5	2
β-strand	472-474	3	6
α-helix	479-481	3
β-strand	483	1	7
β-strand	487	1	7
β-strand	490-492	3	6
β-strand	495-500	6	2
α-helix	502-504	3
α-helix	505-523	19
β-strand	526-532	7	2
α-helix	542-558	17
β-strand	563-566	4	2
β-strand	571	1	8
β-strand	574	1	8
β-strand	576-582	7	2
β-strand	588-597	10	2
α-helix	599-603	5
β-strand	608-609	2	5
β-strand	616-617	2	5
α-helix	618-619	2
β-strand	620-625	6	2
α-helix	630-640	11
α-helix	647-649	3
β-strand	654-658	5	9
α-helix	661-663	3
α-helix	664-675	12
β-strand	681-683	3	9
α-helix	691-700	10
β-strand	705-709	5	9
α-helix	711-716	6
β-strand	718-723	6	9
β-strand	728-733	6	9
α-helix	734-746	13

Chain B: 22 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	356-362	7
β-strand	366-367	2	3
β-strand	377-378	2	3
α-helix	380-400	21
β-strand	403-404	2	10
β-strand	406	1	1
β-strand	410-412	3	11
α-helix	413-419	7
α-helix	421-425	5
α-helix	426-428	3
β-strand	431-434	4	11
β-strand	437-441	5	11
α-helix	446-453	8
β-strand	459	1	12
α-helix	460-462	3
α-helix	463	1
β-strand	465-469	5	10
β-strand	472-474	3	13
α-helix	479-481	3
β-strand	483	1	14
β-strand	487	1	14
β-strand	490-492	3	13
β-strand	495-500	6	10
α-helix	502-504	3
α-helix	505-523	19
β-strand	526-532	7	10
α-helix	542-558	17
β-strand	563-566	4	10
β-strand	576-582	7	10
β-strand	588-597	10	10
α-helix	600-603	4
β-strand	608	1	15
β-strand	609	1	12
α-helix	615-616	2
β-strand	617	1	15
α-helix	618-619	2
β-strand	620-625	6	10
α-helix	630-641	12
α-helix	647-649	3
β-strand	654-658	5	16
α-helix	661-663	3
α-helix	664-676	13
β-strand	681-683	3	16
α-helix	691-700	10
β-strand	705-709	5	16
α-helix	711-716	6
β-strand	718-723	6	16
β-strand	728-733	6	16
α-helix	734-746	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Threonine--tRNA ligase, cytoplasmic	A, B	protein	413	Homo sapiens	P26639 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4HWT_1 Threonine--tRNA ligase, cytoplasmic (chains A, B)
MARDHRKIGRDQELYFFHELSPGSCFFLPKGAYIYNALIEFIRSEYRKRGFQEVVTPNIF
NSRLWMTSGHWQHYSENMFSFEVEKELFALKPMNCPGHCLMFDHRPRSWRELPLRLADFG
VLHRNELSGALTGLTRVRRFQQDDAHIFCAMEQIEDEIKGCLDFLRTVYSVFGFSFKLNL
STRPEKFLGDIEVWDQAEKQLENSLNEFGEKWELNSGDGAFYGPKIDIQIKDAIGRYHQC
ATIQLDFQLPIRFNLTYVSHDGDDKKRPVIVHRAILGSVERMIAILTENYGGKWPFWLSP
RQVMVVPVGPTCDEYAQKVRQQFHDAKFMADIDLDPGCTLNKKIRNAQLAQYNFILVVGE
KEKISGTVNIRTRDNKVHGERTISETIERLQQLKEFRSKQAEEEFLEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
1B2	N-{[3-(2H-indazol-5-yl)phenyl]sulfonyl}-L-threoninamide	C17 H18 N4 O4 S	2
ZN	Zinc ion	Zn	2

Primary citation

Identification of bacteria-selective threonyl-tRNA synthetase substrate inhibitors by structure-based design. Teng, M., Hilgers, M.T., Cunningham, M.L. et al. J Med Chem (2013) 56:1748-1760. DOI 10.1021/jm301756m · PubMed

Other PDB entries of the same protein (UniProt P26639 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5XLN 1.9 Å, Crystal structure of the TRS_UNE-T and 4EHP complex
4P3N 2.6 Å, Structural Basis for Full-Spectrum Inhibition of Threonyl-tRNA Synthetase by Borrelidin 1
4TTV 2.8 Å, Crystal structure of human ThrRS complexing with a bioengineered macrolide BC194
1WWT Solution structure of the TGS domain from human threonyl-tRNA synthetase

Browse structure collections

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