8XP4: Human lysyl-tRNA synthetase with acetyllysine

Crystal Structure of human lysyl-tRNA synthetase with acetyllysine. Determined by X-ray diffraction at 2.26 Å resolution. Released 22 Jan 2025.

Method: X-ray diffraction
Resolution: 2.26 Å
Organism: Homo sapiens
Chains: 2
Atoms: 8,173
Mol. weight: 120.77 kDa
Ligands: ALY
Released: 22 Jan 2025

Explore 8XP4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8XP4 contains 55 α-helices and 46 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: 27 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	73-89	17
α-helix	105-112	8
α-helix	115-116	2
β-strand	120	1	1
β-strand	126-137	12	1
β-strand	142-149	8	1
β-strand	152-159	8	1
α-helix	160-162	3
α-helix	166-175	10
β-strand	181-190	10	1
β-strand	196-207	12	1
α-helix	212-215	4
α-helix	223-228	6
α-helix	230-236	7
α-helix	238-259	22
α-helix	263	1
β-strand	264-265	2	2
β-strand	271-272	2	3
α-helix	281-283	3
β-strand	284-287	4	3
β-strand	292-296	5	3
α-helix	301-310	10
β-strand	314-322	9	2
β-strand	328	1	4
β-strand	331	1	4
β-strand	334-343	10	2
α-helix	349-366	18
β-strand	370-373	4	5
β-strand	383-386	4	5
α-helix	388	1
α-helix	391	1
β-strand	392-395	4	2
α-helix	396-404	9
α-helix	407-410	4
α-helix	411-413	3
α-helix	417-429	13
α-helix	440-451	12
α-helix	453-455	3
β-strand	460-463	4	2
β-strand	466	1	6
β-strand	482	1	6
β-strand	485-490	6	2
β-strand	493-500	8	2
α-helix	501-502	2
α-helix	505-517	13
α-helix	531-540	10
α-helix	541-542	2
β-strand	544-550	7	2
α-helix	551-558	8
α-helix	564-566	3

Chain B: 28 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	73-89	17
α-helix	105-112	8
α-helix	115-116	2
β-strand	120	1	7
β-strand	126-137	12	7
β-strand	142-149	8	7
β-strand	152-159	8	7
α-helix	166-173	8
β-strand	181-190	10	7
β-strand	196-207	12	7
α-helix	212-215	4
α-helix	223-228	6
α-helix	230-236	7
α-helix	238-260	23
β-strand	264-265	2	8
β-strand	271-272	2	3
α-helix	281-283	3
β-strand	284-287	4	3
β-strand	292-296	5	3
α-helix	301-309	9
β-strand	314-322	9	8
β-strand	328	1	9
β-strand	331	1	9
β-strand	334-343	10	8
α-helix	349-366	18
β-strand	370-373	4	10
α-helix	381-382	2
β-strand	383-386	4	10
α-helix	388	1
α-helix	391	1
β-strand	392-395	4	8
α-helix	396-404	9
α-helix	407-410	4
α-helix	411-413	3
α-helix	417-429	13
α-helix	435	1
α-helix	437	1
α-helix	440-451	12
α-helix	453-455	3
β-strand	460-463	4	8
β-strand	466	1	11
β-strand	482	1	11
β-strand	485-490	6	8
β-strand	493-500	8	8
α-helix	501-502	2
α-helix	505-511	7
α-helix	531-538	8
α-helix	541-542	2
β-strand	544-550	7	8
α-helix	551-558	8
α-helix	564-566	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine--tRNA ligase	A, B	protein	520	Homo sapiens	Q15046 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8XP4_1 Lysine--tRNA ligase (chains A, B)
MSVDPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDHLTDITLKV
AGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFIHINNKLRRGDIIGVQGNP
GKTKKGELSIIPYEITLLSPCLHMLPHLHFGLKDKETRYRQRYLDLILNDFVRQKFIIRS
KIITYIRSFLDELGFLEIETPMMNIIPGGAVAKPFITYHNELDMNLYMRIAPELYHKMLV
VGGIDRVYEIGRQFRNEGIDLTHNPEFTTCEFYMAYADYHDLMEITEKMVSGMVKHITGS
YKVTYHPDGPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETRKILDDICV
AKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSPLAKWHRSKEGLTERFEL
FVMKKEICNAYTELNDPMRQRQLFEEQAKAKAAGDDEAMFIDENFCTALEYGLPPTAGWG
MGIDRVAMFLTDSNNIKEVLLFPAMKPEDKKELEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
ALY	N(6)-acetyllysine	C8 H16 N2 O3	2

Primary citation

Co-Translational Deposition of N6-Acetyl-L-Lysine in Nascent Proteins Contributes to the Acetylome in Mammalian Cells. Guo, D., Li, N., Zhang, X. et al. Adv Sci (Weinh) (2025) 12:2403309. DOI 10.1002/advs.202403309

Other PDB entries of the same protein (UniProt Q15046 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6ILD 1.88 Å, Crystal Structure of Human LysRS: P38/AIMP2 Complex II
4YCU 2.1 Å, Crystal structure of cladosporin in complex with human lysyl-tRNA synthetase
3BJU 2.31 Å, Crystal Structure of tetrameric form of human lysyl-tRNA synthetase
6CHD 2.5 Å, Crystal Structure of Human Lysyl-tRNA Synthetase complexed with L-Lysylsulfamoyl Adenosine
7EA9 2.5 Å, Crystal Structure of human lysyl-tRNA synthetase Y145H mutant
6ILH 2.5 Å, Crystal Structure of human lysyl-tRNA synthetase L350H mutant
8HYR 2.55 Å, Crystal structure of human KARS apo
9DPL 2.8 Å, Human LysRS bound to cellular modified tRNA-Lys3 and AIMP2
4DPG 2.84 Å, Crystal Structure of Human LysRS: P38/AIMP2 Complex I
4YCW 2.9 Å, Crystal structure of cladosporin in complex with plasmodium like human lysyl-tRNA…
9DPB 2.9 Å, Human LysRS bound to unmodified tRNA-Lys3 (Undocked State, AMPCPP bound)
9DPA 3.0 Å, Human LysRS bound to unmodified tRNA-Lys3 (3'-CCA Docked State, AMP bound)

Browse structure collections

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