4P3N: Threonine--tRNA ligase, cytoplasmic

Structural Basis for Full-Spectrum Inhibition of Threonyl-tRNA Synthetase by Borrelidin 1. Determined by X-ray diffraction at 2.6 Å resolution. Released 11 Mar 2015.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 13,506
Mol. weight: 196.09 kDa
Ligands: ZN, 2CR
Released: 11 Mar 2015

Explore 4P3N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4P3N contains 73 α-helices and 119 β-strands across 4 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: 18 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	323-329	7
β-strand	333-334	2	1
β-strand	344-345	2	1
α-helix	347-367	21
β-strand	370-371	2	2
β-strand	373	1	3
β-strand	377-379	3	4
α-helix	380-386	7
α-helix	388-391	4
α-helix	393-395	3
β-strand	398-401	4	4
β-strand	404-408	5	4
α-helix	413-420	8
β-strand	426	1	5
α-helix	427-429	3
β-strand	432-436	5	2
β-strand	439-441	3	6
β-strand	450	1	7
β-strand	454	1	7
β-strand	457-459	3	6
β-strand	460	1	8
β-strand	462-467	6	2
α-helix	469-471	3
α-helix	472-490	19
β-strand	493-499	7	2
α-helix	509-526	18
β-strand	530-533	4	2
β-strand	538	1	9
β-strand	541	1	9
β-strand	543-549	7	2
β-strand	555-564	10	2
α-helix	566-570	5
β-strand	575	1	10
β-strand	576	1	5
β-strand	584	1	10
β-strand	587-592	6	2
β-strand	596	1	8
α-helix	597-608	12
β-strand	621-625	5	11
α-helix	628-630	3
α-helix	631-643	13
β-strand	648-650	3	11
α-helix	658-667	10
β-strand	672-676	5	11
α-helix	678-683	6
β-strand	685-690	6	11
β-strand	695-700	6	11
α-helix	701-713	13
α-helix	719-722	4

Chain B: 19 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	323-329	7
β-strand	333-334	2	3
β-strand	344-345	2	3
α-helix	347-367	21
β-strand	370-371	2	12
β-strand	373	1	1
β-strand	377-379	3	13
α-helix	380-386	7
α-helix	388-391	4
α-helix	393-395	3
β-strand	398-401	4	13
β-strand	404-408	5	13
α-helix	413-420	8
β-strand	426	1	14
α-helix	427-429	3
β-strand	432-436	5	12
β-strand	439-441	3	15
α-helix	446-448	3
β-strand	450	1	16
β-strand	454	1	16
β-strand	457-459	3	15
β-strand	462-467	6	12
α-helix	469-471	3
α-helix	472-490	19
β-strand	493-499	7	12
α-helix	509-526	18
β-strand	530-533	4	12
β-strand	538	1	17
β-strand	541	1	17
β-strand	543-549	7	12
β-strand	555-564	10	12
α-helix	566-570	5
β-strand	575	1	18
β-strand	576	1	14
β-strand	584	1	18
β-strand	587-592	6	12
α-helix	597-608	12
β-strand	621-625	5	19
α-helix	628-630	3
α-helix	631-642	12
β-strand	648-650	3	19
α-helix	658-667	10
β-strand	672-676	5	19
α-helix	678-683	6
β-strand	685-690	6	19
β-strand	695-700	6	19
α-helix	701-713	13
α-helix	719-722	4

Chain C: 17 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	323-329	7
β-strand	333-334	2	20
β-strand	344-345	2	20
α-helix	347-367	21
β-strand	370-371	2	21
β-strand	373	1	22
β-strand	377-379	3	23
α-helix	380-386	7
α-helix	388-391	4
α-helix	393-395	3
β-strand	398-401	4	23
β-strand	404-408	5	23
α-helix	413-420	8
β-strand	426	1	24
β-strand	432-436	5	21
β-strand	439-441	3	25
β-strand	450	1	26
β-strand	454	1	26
β-strand	457-459	3	25
β-strand	460-467	8	21
α-helix	469-471	3
α-helix	472-490	19
β-strand	493-499	7	21
α-helix	509-526	18
β-strand	530-533	4	21
β-strand	538	1	27
β-strand	541	1	27
β-strand	543-549	7	21
β-strand	555-564	10	21
α-helix	566-570	5
β-strand	575	1	28
β-strand	576	1	24
β-strand	584	1	28
β-strand	587-596	10	21
α-helix	597-608	12
β-strand	621-625	5	29
α-helix	628-630	3
α-helix	631-643	13
β-strand	648-650	3	29
α-helix	658-667	10
β-strand	672-676	5	29
α-helix	678-683	6
β-strand	685-690	6	29
β-strand	695-700	6	29
α-helix	701-713	13
α-helix	719-722	4

Chain D: 19 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	323-329	7
β-strand	333-334	2	22
β-strand	344-345	2	22
α-helix	347-367	21
β-strand	370-371	2	30
β-strand	373	1	20
β-strand	377-379	3	31
α-helix	380-386	7
α-helix	388-391	4
α-helix	393-395	3
β-strand	398-401	4	31
β-strand	404-408	5	31
α-helix	413-420	8
β-strand	425-426	2	32
β-strand	432-436	5	30
α-helix	438	1
β-strand	439-441	3	33
β-strand	450	1	34
β-strand	454	1	34
β-strand	457-459	3	33
β-strand	460	1	35
β-strand	462-467	6	30
α-helix	469-471	3
α-helix	472-490	19
β-strand	493-499	7	30
α-helix	509-526	18
β-strand	530-533	4	30
β-strand	538	1	36
β-strand	541	1	36
β-strand	543-549	7	30
β-strand	555-564	10	30
α-helix	566-570	5
β-strand	575-576	2	32
β-strand	584	1	32
β-strand	587-592	6	30
β-strand	596	1	35
α-helix	597-608	12
α-helix	614-616	3
β-strand	621-625	5	37
α-helix	628-630	3
α-helix	631-642	12
β-strand	648-650	3	37
α-helix	658-667	10
β-strand	672-676	5	37
α-helix	678-683	6
β-strand	685-690	6	37
β-strand	695-700	6	37
α-helix	701-713	13
α-helix	719-722	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Threonine--tRNA ligase, cytoplasmic	A, B, C, D	protein	415	Homo sapiens	P26639 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>4P3N_1 Threonine--tRNA ligase, cytoplasmic (chains A, B, C, D)
MGSSHHHHHHSSGDHRKIGRDQELYFFHELSPGSCFFLPKGAYIYNALIEFIRSEYRKRG
FQEVVTPNIFNSRLWMTSGHWQHYSENMFSFEVEKELFALKPMNCPGHCLMFDHRPRSWR
ELPLRLADFGVLHRNELSGALTGLTRVRRFQQDDAHIFCAMEQIEDEIKGCLDFLRTVYS
VFGFSFKLNLSTRPEKFLGDIEVWDQAEKQLENSLNEFGEKWELNSGDGAFYGPKIDIQI
KDAIGRYHQCATIQLDFQLPIRFNLTYVSHDGDDKKRPVIVHRAILGSVERMIAILTENY
GGKWPFWLSPRQVMVVPVGPTCDEYAQKVRQQFHDAKFMADIDLDPGCTLNKKIRNAQLA
QYNFILVVGEKEKISGTVNIRTRDNKVHGERTISETIERLQQLKEFRSKQAEEEF

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
2CR	(1R,2R)-2-[(2S,4E,6E,8R,9S,11R,13S,15S,16S)-7-cyano-8,16-dihydroxy-9,11,13,15-t…	C28 H43 N O6	4

Primary citation

Structural basis for full-spectrum inhibition of translational functions on a tRNA synthetase. Fang, P., Yu, X., Jeong, S.J. et al. Nat Commun (2015) 6:6402-6402. DOI 10.1038/ncomms7402 · 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
4HWT 2.3 Å, Crystal structure of human Threonyl-tRNA synthetase bound to a novel inhibitor
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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