4YCW: Cladosporin
Crystal structure of cladosporin in complex with plasmodium like human lysyl-tRNA synthetase mutant. Determined by X-ray diffraction at 2.9 Å resolution. Released 10 Jun 2015.
- Method
- X-ray diffraction
- Resolution
- 2.9 Å
- Organism
- Homo sapiens
- Chains
- 8
- Atoms
- 16,000
- Mol. weight
- 258.21 kDa
- Ligands
- LYS, KRS
- Released
- 10 Jun 2015
Explore 4YCW in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4YCW contains 118 α-helices and 106 β-strands across 7 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: 29 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 | 126-139 | 14 | 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 | 212-214 | 3 | |
| 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 | 284-286 | 3 | 3 |
| β-strand | 293-296 | 4 | 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 | 411-413 | 3 | |
| 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 | 505-521 | 17 | |
| α-helix | 527-529 | 3 | |
| α-helix | 531-538 | 8 | |
| β-strand | 544-550 | 7 | 2 |
| α-helix | 551-558 | 8 | |
| α-helix | 564-566 | 3 | |
Chain B: 29 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 | 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 | 505-519 | 15 | |
| α-helix | 527-529 | 3 | |
| α-helix | 531-538 | 8 | |
| β-strand | 544-550 | 7 | 10 |
| α-helix | 551-558 | 8 | |
| α-helix | 564-566 | 3 | |
Chains C and D: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-5 | 3 | |
Chain E: 28 helices, 27 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 73-89 | 17 | |
| α-helix | 108-111 | 4 | |
| α-helix | 115-116 | 2 | |
| β-strand | 120 | 1 | 16 |
| β-strand | 126-137 | 12 | 16 |
| β-strand | 142-149 | 8 | 16 |
| β-strand | 152-159 | 8 | 16 |
| α-helix | 166-175 | 10 | |
| β-strand | 181-190 | 10 | 16 |
| β-strand | 196-207 | 12 | 16 |
| 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 | 17 |
| β-strand | 271-272 | 2 | 18 |
| α-helix | 281-283 | 3 | |
| β-strand | 284-287 | 4 | 18 |
| β-strand | 292-296 | 5 | 18 |
| α-helix | 301-309 | 9 | |
| β-strand | 314-322 | 9 | 17 |
| β-strand | 328 | 1 | 19 |
| β-strand | 331 | 1 | 19 |
| β-strand | 334-343 | 10 | 17 |
| α-helix | 347-366 | 20 | |
| β-strand | 370-373 | 4 | 20 |
| β-strand | 383-386 | 4 | 20 |
| α-helix | 388 | 1 | |
| α-helix | 391 | 1 | |
| β-strand | 392-395 | 4 | 17 |
| α-helix | 396-404 | 9 | |
| α-helix | 407-410 | 4 | |
| α-helix | 411-413 | 3 | |
| α-helix | 417-430 | 14 | |
| α-helix | 435 | 1 | |
| α-helix | 440-451 | 12 | |
| β-strand | 460-463 | 4 | 17 |
| β-strand | 466 | 1 | 21 |
| α-helix | 467-469 | 3 | |
| β-strand | 473 | 1 | 22 |
| α-helix | 474 | 1 | |
| β-strand | 475 | 1 | 23 |
| α-helix | 476 | 1 | |
| β-strand | 482 | 1 | 21 |
| β-strand | 483 | 1 | 23 |
| β-strand | 485-490 | 6 | 17 |
| β-strand | 493-500 | 8 | 17 |
| β-strand | 501 | 1 | 22 |
| α-helix | 505-520 | 16 | |
| α-helix | 527-529 | 3 | |
| α-helix | 531-538 | 8 | |
| β-strand | 544-550 | 7 | 17 |
| α-helix | 551-559 | 9 | |
| α-helix | 564-566 | 3 | |
Chain F: 29 helices, 25 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 73-89 | 17 | |
| α-helix | 105-112 | 8 | |
| α-helix | 115-116 | 2 | |
| β-strand | 126-132 | 7 | 24 |
| β-strand | 136-137 | 2 | 24 |
| β-strand | 142-149 | 8 | 24 |
| β-strand | 152-159 | 8 | 24 |
| α-helix | 166-175 | 10 | |
| β-strand | 181-190 | 10 | 24 |
| β-strand | 196-207 | 12 | 24 |
| α-helix | 212-214 | 3 | |
| α-helix | 223-228 | 6 | |
| α-helix | 230-236 | 7 | |
| α-helix | 238-260 | 23 | |
| β-strand | 264-265 | 2 | 25 |
| β-strand | 271-272 | 2 | 18 |
| α-helix | 281-283 | 3 | |
| β-strand | 284-287 | 4 | 18 |
| β-strand | 292-296 | 5 | 18 |
| α-helix | 297 | 1 | |
| α-helix | 301-309 | 9 | |
| β-strand | 314-322 | 9 | 25 |
| β-strand | 334-343 | 10 | 25 |
| α-helix | 347-366 | 20 | |
| β-strand | 370-373 | 4 | 26 |
| β-strand | 383-386 | 4 | 26 |
| α-helix | 388 | 1 | |
| α-helix | 391 | 1 | |
| β-strand | 392-395 | 4 | 25 |
| α-helix | 396-403 | 8 | |
| α-helix | 411-413 | 3 | |
| α-helix | 417-430 | 14 | |
| α-helix | 435 | 1 | |
| α-helix | 438 | 1 | |
| α-helix | 440-451 | 12 | |
| β-strand | 460-463 | 4 | 25 |
| β-strand | 466 | 1 | 27 |
| α-helix | 467-469 | 3 | |
| β-strand | 473 | 1 | 28 |
| α-helix | 474 | 1 | |
| β-strand | 475 | 1 | 29 |
| α-helix | 476 | 1 | |
| β-strand | 482 | 1 | 27 |
| β-strand | 483 | 1 | 29 |
| β-strand | 485-490 | 6 | 25 |
| β-strand | 493-500 | 8 | 25 |
| β-strand | 501 | 1 | 28 |
| α-helix | 505-518 | 14 | |
| α-helix | 519-523 | 5 | |
| α-helix | 527-529 | 3 | |
| α-helix | 531-538 | 8 | |
| β-strand | 544-550 | 7 | 25 |
| α-helix | 551-558 | 8 | |
| α-helix | 564-566 | 3 | |
Chain H: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-8 | 3 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Lysine--tRNA ligase | A, B, E, F | protein | 513 | Homo sapiens | Q15046 (AlphaFold model) |
| Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 | C, D, G, H | protein | 42 | Homo sapiens | Q13155 (AlphaFold model) |
Sequence of entity 1 (A, B, E, F), FASTA
>4YCW_1 Lysine--tRNA ligase (chains A, B, E, F)
MSVDPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDHLTDITLKV
AGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFIHINNKLRRGDIIGVQGNP
GKTKKGELSIIPYEITLLSPCLHMLPHLHFGLKDKETRYRQRYLDLILNDFVRQKFIIRS
KIITYIRSFLDELGFLEIETPMMNIIPGGAVAKPFITYHNELDMNLYMRIATELYHKMLV
VGGIDRVYEIGRVFRNEGIDLTHNPEFTSCEFYMAYADYHDLMEITEKMVSGMVKHITGS
YKVTYHPDGPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETRKILDDICV
AKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSPLAKWHRSKEGLTERFEL
FVMKKEICNAYTELNDPMRQRQLFEEQAKAKAAGDDEAMFIDENFCTALEYGLPPTAGWG
MGIDRVAMFLTDSNNIKEVLLFPAMKPEDKKEN
Sequence of entity 2 (C, D, G, H), FASTA
>4YCW_2 Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (chains C, D, G, H)
MPMYQVKPYHGGGAPLRVELPTCMYRLPNVHGRSYGHHHHHH
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| LYS | Lysine | C6 H15 N2 O2 | 4 |
| KRS | cladosporin | C16 H20 O5 | 4 |
Primary citation
Structural Basis for Specific Inhibition of tRNA Synthetase by ATP Competitive Inhibitor. Fang, P., Han, H., Wang, J. et al. Chem Biol (2015) 22:1.
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
- 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
- 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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