6CHD: Human Lysyl-tRNA Synthetase

Crystal Structure of Human Lysyl-tRNA Synthetase complexed with L-Lysylsulfamoyl Adenosine. Determined by X-ray diffraction at 2.5 Å resolution. Released 7 Mar 2018.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 8,425
Mol. weight: 138.45 kDa
Ligands: KAA
Released: 7 Mar 2018

Explore 6CHD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6CHD contains 61 α-helices and 54 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: 30 helices, 27 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	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	238-260	23
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	301-309	9
β-strand	314-322	9	2
β-strand	328	1	4
β-strand	331	1	4
β-strand	334-343	10	2
α-helix	347-366	20
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	407-409	3
α-helix	411-413	3
α-helix	417-430	14
α-helix	435	1
α-helix	440-451	12
α-helix	453-455	3
β-strand	460-463	4	2
β-strand	466	1	6
α-helix	467-469	3
β-strand	473	1	7
α-helix	474	1
β-strand	475	1	8
α-helix	476	1
β-strand	482	1	6
β-strand	483	1	8
β-strand	485-490	6	2
β-strand	493-500	8	2
β-strand	501	1	7
α-helix	502	1
α-helix	505-520	16
α-helix	526-528	3
α-helix	531-537	7
β-strand	544-550	7	2
α-helix	551-558	8
α-helix	564-567	4

Chain B: 31 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	73-90	18
α-helix	105-112	8
α-helix	115-116	2
β-strand	120	1	9
β-strand	126-137	12	9
β-strand	142-149	8	9
β-strand	152-159	8	9
α-helix	166-175	10
β-strand	181-190	10	9
β-strand	196-207	12	9
α-helix	223-228	6
α-helix	230-236	7
α-helix	238-260	23
α-helix	263	1
β-strand	264-265	2	10
β-strand	271-272	2	11
α-helix	281-283	3
β-strand	284-287	4	11
β-strand	292-296	5	11
α-helix	301-309	9
β-strand	314-322	9	10
β-strand	328	1	12
β-strand	331	1	12
β-strand	334-343	10	10
α-helix	347-366	20
β-strand	370-373	4	13
β-strand	383-386	4	13
α-helix	388	1
α-helix	391	1
β-strand	392-395	4	10
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	10
β-strand	466	1	14
α-helix	467-469	3
β-strand	473	1	15
α-helix	474	1
β-strand	475	1	16
α-helix	476	1
β-strand	482	1	14
β-strand	483	1	16
β-strand	485-490	6	10
β-strand	493-500	8	10
β-strand	501	1	15
α-helix	502	1
α-helix	505-520	16
α-helix	526-529	4
α-helix	531-538	8
α-helix	541-542	2
β-strand	544-550	7	10
α-helix	551-558	8
α-helix	564-567	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine--tRNA ligase	A, B	protein	597	Homo sapiens	Q15046 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6CHD_1 Lysine--tRNA ligase (chains A, B)
MAAVQAAEVKVDGSEPKLSKNELKRRLKAEKKVAEKEAKQKELSEKQLSQATAAATNHTT
DNGVGPEEESVDPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDH
LTDITLKVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFIHINNKLRRGD
IIGVQGNPGKTKKGELSIIPYEITLLSPCLHMLPHLHFGLKDKETRYRQRYLDLILNDFV
RQKFIIRSKIITYIRSFLDELGFLEIETPMMNIIPGGAVAKPFITYHNELDMNLYMRIAP
ELYHKMLVVGGIDRVYEIGRQFRNEGIDLTHNPEFTTCEFYMAYADYHDLMEITEKMVSG
MVKHITGSYKVTYHPDGPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETR
KILDDICVAKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSPLAKWHRSKE
GLTERFELFVMKKEICNAYTELNDPMRQRQLFEEQAKAKAAGDDEAMFIDENFCTALEYG
LPPTAGWGMGIDRVAMFLTDSNNIKEVLLFPAMKPEDKKENVATTDTLESTTVGTSV

Ligands and cofactors

ID	Name	Formula	Copies
KAA	5'-O-[(L-lysylamino)sulfonyl]adenosine	C16 H26 N8 O7 S	2

Water and common crystallization additives (SO4, EDO, GOL) are not listed.

Primary citation

Crystal Structure of Human Lysyl-tRNA Synthetase complexed with L-Lysylsulfamoyl Adenosine. Dranow, D.M., Abendroth, J., Baragana, B. et al. To be published.

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
8XP4 2.26 Å, Crystal Structure of human lysyl-tRNA synthetase with acetyllysine
3BJU 2.31 Å, Crystal Structure of tetrameric form of human lysyl-tRNA synthetase
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)

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