4YCU: Cladosporin

Crystal structure of cladosporin in complex with human lysyl-tRNA synthetase. Determined by X-ray diffraction at 2.1 Å resolution. Released 10 Jun 2015.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 3
Atoms: 9,044
Mol. weight: 124.64 kDa
Ligands: LYS, KRS
Released: 10 Jun 2015

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

Secondary structure: helices and β-sheets

4YCU contains 62 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: 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	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	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	505-519	15
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: 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	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	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	42	Homo sapiens	Q13155 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4YCU_1 Lysine--tRNA ligase (chains A, B)
MSVDPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDHLTDITLKV
AGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFIHINNKLRRGDIIGVQGNP
GKTKKGELSIIPYEITLLSPCLHMLPHLHFGLKDKETRYRQRYLDLILNDFVRQKFIIRS
KIITYIRSFLDELGFLEIETPMMNIIPGGAVAKPFITYHNELDMNLYMRIAPELYHKMLV
VGGIDRVYEIGRQFRNEGIDLTHNPEFTTCEFYMAYADYHDLMEITEKMVSGMVKHITGS
YKVTYHPDGPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETRKILDDICV
AKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSPLAKWHRSKEGLTERFEL
FVMKKEICNAYTELNDPMRQRQLFEEQAKAKAAGDDEAMFIDENFCTALEYGLPPTAGWG
MGIDRVAMFLTDSNNIKEVLLFPAMKPEDKKEN

Sequence of entity 2 (C), FASTA

>4YCU_2 Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (chains C)
MPMYQVKPYHGGGAPLRVELPTCMYRLPNVHGRSYGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
LYS	Lysine	C6 H15 N2 O2	2
KRS	cladosporin	C16 H20 O5	2

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

Primary citation

Structural Basis for Specific Inhibition of tRNA Synthetase by an ATP Competitive Inhibitor. Fang, P., Han, H., Wang, J. et al. Chem Biol (2015) 22:734-744. DOI 10.1016/j.chembiol.2015.05.007 · PubMed

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
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)

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