6ILD: Human LysRS: P38/AIMP2 Complex II

Crystal Structure of Human LysRS: P38/AIMP2 Complex II. Determined by X-ray diffraction at 1.88 Å resolution. Released 27 Feb 2019.

Method: X-ray diffraction
Resolution: 1.88 Å
Organism: Homo sapiens
Chains: 3
Atoms: 9,203
Mol. weight: 124.78 kDa
Ligands: LYS, 45A, MG
Released: 27 Feb 2019

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

Secondary structure: helices and β-sheets

6ILD contains 64 α-helices and 54 β-strands across 3 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: 31 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	160-162	3
α-helix	166-175	10
β-strand	181-190	10	1
β-strand	196-207	12	1
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	407-410	4
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	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	527-529	3
α-helix	531-538	8
α-helix	541-542	2
β-strand	544-550	7	2
α-helix	551-558	8
α-helix	564-567	4

Chain B: 32 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	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	212-214	3
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	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	10
β-strand	328	1	11
β-strand	331	1	11
β-strand	334-343	10	10
α-helix	347-366	20
β-strand	370-373	4	12
β-strand	383-386	4	12
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	13
α-helix	467-469	3
β-strand	473	1	14
α-helix	474	1
β-strand	475	1	15
α-helix	476	1
β-strand	482	1	13
β-strand	483	1	15
β-strand	485-490	6	10
β-strand	493-500	8	10
β-strand	501	1	14
α-helix	502	1
α-helix	505-521	17
α-helix	527-529	3
α-helix	531-537	7
α-helix	541-542	2
β-strand	544-550	7	10
α-helix	551-558	8
α-helix	564-567	4

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine--tRNA ligase	A, B	protein	513	Homo sapiens	Q15046 (AlphaFold model)
Aminoacyl tRNA synthase complex-interacting multifunctional protein 2	C	protein	44	Homo sapiens	Q13155 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6ILD_1 Lysine--tRNA ligase (chains A, B)
MSVDPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDHLTDITLKV
AGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFIHINNKLRRGDIIGVQGNP
GKTKKGELSIIPYEITLLSPCLHMLPHLHFGLKDKETRYRQRYLDLILNDFVRQKFIIRS
KIITYIRSFLDELGFLEIETPMMNIIPGGAVAKPFITYHNELDMNLYMRIAPELYHKMLV
VGGIDRVYEIGRQFRNEGIDLTHNPEFTTCEFYMAYADYHDLMEITEKMVSGMVKHITGS
YKVTYHPDGPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETRKILDDICV
AKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSPLAKWHRSKEGLTERFEL
FVMKKEICNAYTELNDPMRQRQLFEEQAKAKAAGDDEAMFIDENFCTALEYGLPPTAGWG
MGIDRVAMFLTDSNNIKEVLLFPAMKPEDKKEN

Sequence of entity 2 (C), FASTA

>6ILD_2 Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (chains C)
MPMYQVKPYHGGGAPLRVELPTCMYRLPNVHGRSYGLEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
LYS	Lysine	C6 H15 N2 O2	2
45A	5'-O-[(S)-hydroxy(methyl)phosphoryl]adenosine	C11 H16 N5 O6 P	1
MG	Magnesium ion	Mg	2

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

Primary citation

Retractile lysyl-tRNA synthetase-AIMP2 assembly in the human multi-aminoacyl-tRNA synthetase complex. Hei, Z., Wu, S., Liu, Z. et al. J Biol Chem (2019) 294:4775-4783. DOI 10.1074/jbc.RA118.006356 · PubMed

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

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
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

About this viewer

MolViewer shows 6ILD directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.