5Y6L: Methionine--tRNA ligase, cytoplasmic
A subcomplex crystal structure of human cytosolic aspartyl-tRNA synthetase and heterotetrameric glutathione transferase-homology domains in multi-tRNA synthetase complex. Determined by X-ray diffraction at 2.9 Å resolution. Released 15 Aug 2018.
- Method
- X-ray diffraction
- Resolution
- 2.9 Å
- Organism
- Homo sapiens
- Chains
- 5
- Atoms
- 6,458
- Mol. weight
- 152.86 kDa
- Ligands
- PO4
- Released
- 15 Aug 2018
Explore 5Y6L in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5Y6L contains 50 α-helices and 21 β-strands across 5 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: 15 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-5 | 4 | 1 |
| α-helix | 12-19 | 8 | |
| α-helix | 20-22 | 3 | |
| β-strand | 29-32 | 4 | 1 |
| β-strand | 50-52 | 3 | 1 |
| β-strand | 58-59 | 2 | 1 |
| α-helix | 62-72 | 11 | |
| α-helix | 79-87 | 9 | |
| α-helix | 88-92 | 5 | |
| α-helix | 93-104 | 12 | |
| α-helix | 111-114 | 4 | |
| α-helix | 118-131 | 14 | |
| α-helix | 143-156 | 14 | |
| α-helix | 159-161 | 3 | |
| α-helix | 167-178 | 12 | |
| α-helix | 180-190 | 11 | |
| α-helix | 194-197 | 4 | |
| α-helix | 199-203 | 5 | |
| α-helix | 206-207 | 2 | |
Chain B: 11 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-13 | 11 | |
| β-strand | 22-23 | 2 | 2 |
| β-strand | 32-34 | 3 | 2 |
| β-strand | 40-42 | 3 | 2 |
| α-helix | 44-54 | 11 | |
| α-helix | 58-61 | 4 | |
| α-helix | 65-77 | 13 | |
| α-helix | 78-82 | 5 | |
| α-helix | 88-102 | 15 | |
| α-helix | 115-128 | 14 | |
| α-helix | 133-138 | 6 | |
| α-helix | 140-150 | 11 | |
| α-helix | 153-156 | 4 | |
| α-helix | 160-163 | 4 | |
Chain C: 9 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-9 | 5 | 3 |
| α-helix | 15-24 | 10 | |
| β-strand | 31-35 | 5 | 3 |
| β-strand | 39-43 | 5 | 3 |
| β-strand | 46-48 | 3 | 3 |
| α-helix | 51-61 | 11 | |
| α-helix | 63-65 | 3 | |
| α-helix | 72-86 | 15 | |
| α-helix | 95-106 | 12 | |
| α-helix | 119-129 | 11 | |
| α-helix | 132-138 | 7 | |
| α-helix | 145-155 | 11 | |
| α-helix | 158-166 | 9 | |
Chain D: 12 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 107-109 | 3 | |
| β-strand | 120-126 | 7 | 4 |
| α-helix | 133-142 | 10 | |
| β-strand | 148-155 | 8 | 4 |
| α-helix | 163-166 | 4 | |
| β-strand | 183-189 | 7 | 4 |
| β-strand | 196-198 | 3 | 4 |
| α-helix | 204-206 | 3 | |
| β-strand | 207-208 | 2 | 4 |
| α-helix | 210-219 | 10 | |
| α-helix | 222-224 | 3 | |
| α-helix | 227-239 | 13 | |
| α-helix | 240-244 | 5 | |
| α-helix | 249-265 | 17 | |
| β-strand | 268 | 1 | 5 |
| β-strand | 271 | 1 | 5 |
| α-helix | 276-287 | 12 | |
| α-helix | 297-308 | 12 | |
| α-helix | 310-320 | 11 | |
Chain E: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 340-341 | 2 | 4 |
| α-helix | 343 | 1 | |
| β-strand | 344-346 | 3 | 6 |
| α-helix | 348-357 | 10 | |
| α-helix | 370-384 | 15 | |
| β-strand | 389-391 | 3 | 6 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Methionine--tRNA ligase, cytoplasmic | A | protein | 232 | Homo sapiens | P56192 (AlphaFold model) |
| Eukaryotic translation elongation factor 1 epsilon-1 | B | protein | 186 | Homo sapiens | O43324 (AlphaFold model) |
| Bifunctional glutamate/proline--tRNA ligase | C | protein | 175 | Homo sapiens | P07814 (AlphaFold model) |
| Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 | D | protein | 240 | Homo sapiens | Q13155 (AlphaFold model) |
| Aspartate--tRNA ligase, cytoplasmic | E | protein | 521 | Homo sapiens | P14868 |
Sequence of entity 1 (A), FASTA
>5Y6L_1 Methionine--tRNA ligase, cytoplasmic (chains A)
MRLFVSDGVPGCLPVLAAAGRARGRAEVLISTVGPEDCVVPFLTRPKVPVLQLDSGNYLF
STSAICRYFFLLSGWEQDDLTNQWLEWEATELQPALSAALYYLVVQGKKGEDVLGSVRRA
LTHIDHSLSRQNCPFLAGETESLADIVLWGALYPLLQDPAYLPEELSALHRWFQTLSTQE
PCQRAAETVLKQQGVLALRPYLQKQPQPSPAEGRAVTNEPEEEELEHHHHHH
Sequence of entity 2 (B), FASTA
>5Y6L_2 Eukaryotic translation elongation factor 1 epsilon-1 (chains B)
MRGSHHHHHHGSMAAAAELSLLEKSLGLSKGNKYSAQGERQIPVLQTNNGPSLTGLTTIA
AHLVKQANKEYLLGSTAEEKAIVQQWLEYRVTQVDGHSSKNDIHTLLKDLNSYLEDKVYL
TGYNFTLADILLYYGLHRFIVDLTVQEKEKYLNVSRWFSHIQHYPGIRQHLSSVVFIKNR
LYTNSH
Sequence of entity 3 (C), FASTA
>5Y6L_3 Bifunctional glutamate/proline--tRNA ligase (chains C)
MATLSLTVNSGDPPLGALLAVEHVKDDVSISVEEGKENILHVSENVIFTDVNSILRYLAR
VATTAGLYGSNLMEHTEIDHWLEFSATKLSSSDSFTSTINELNHSLSLRTYLVGNSLSLA
DLSVWATLKGNAAWQEQLKQKKAPVHVKRWFGFLEAQQAFQSVGTKWDVSTTKAR
Sequence of entity 4 (D), FASTA
>5Y6L_4 Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (chains D)
MTNIIQADEPTTLTTNALDLNSVLGKDYGALKDIVINANPASPPLSLLVLHRLLCEHFRV
LSTVHTHSSVKSVPENLLKCFGEQNKKQPRQDYQLGFTLIWKNVPKTQMKFSIQTMCPIE
GEGNIARFLFSLFGQKHNAVNATLIDSWVDIAIFQLKEGSSKEKAAVFRSMNSALGKSPW
LAGNELTVADVVLWSVLQQIGGCSVTVPANVQRWMRSCENLAPFNTALKLLKLEHHHHHH
Sequence of entity 5 (E), FASTA
>5Y6L_5 Aspartate--tRNA ligase, cytoplasmic (chains E)
MGSSHHHHHHSSGLVPRGSHMPSASASRKSQEKPREIMDAAEDYAKERYGISSMIQSQEK
PDRVLVRVRDLTIQKADEVVWVRARVHTSRAKGKQCFLVLRQQQFNVQALVAVGDHASKQ
MVKFAANINKESIVDVEGVVRKVNQKIGSCTQQDVELHVQKIYVISLAEPRLPLQLDDAV
RPEAEGEEEGRATVNQDTRLDNRVIDLRTSTSQAVFRLQSGICHLFRETLINKGFVEIQT
PKIISAASEGGANVFTVSYFKNNAYLAQSPQLYKQMCICADFEKVFSIGPVFRAEDSNTH
RHLTEFVGLDIEMAFNYHYHEVMEEIADTMVQIFKGLQERFQTEIQTVNKQFPCEPFKFL
EPTLRLEYCEALAMLREAGVEMGDEDDLSTPNEKLLGHLVKEKYDTDFYILDKYPLAVRP
FYTMPDPRNPKQSNSYDMFMRGEEILSGAQRIHDPQLLTERALHHGIDLEKIKAYIDSFR
FGAPPHAGGGIGLERVTMLFLGLHNVRQTSMFPRDPKRLTP
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| PO4 | Phosphate ion | O4 P | 2 |
Primary citation
A subcomplex crystal structure of human cytosolic aspartyl-tRNA synthetase and heterotetrameric glutathione transferase-homology domains in multi-tRNA synthetase complex. Cho, H.Y., Lee, H.J., Kang, B.S. To be published.
Other PDB entries of the same protein (UniProt P56192 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 4BVX 1.6 Å, Crystal structure of the AIMP3-MRS N-terminal domain complex with I3C
- 4BL7 1.89 Å, Crystal structure of the AIMP3-MRS N-terminal domain complex in different space group
- 4BVY 1.99 Å, Crystal structure of the AIMP3-MRS N-terminal domain complex
- 5GL7 2.01 Å, Crystal structure of a truncated human cytosolic methionyl-tRNA synthetase
- 5GOY 2.28 Å, The crystal structure of human cytosolic methionyl-tRNA synthetase in complex with…
- 2DJV Solution structures of the WHEP-TRS domain of human methionyl-tRNA synthetase
Browse structure collections
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