MolNFT v1 · #143132 · protein
Crystal structure of lysyl-tRNA synthetase from mycobacterium ulcerans complexed with L-lysine and cladosporin
6AQG · Lysine--tRNA ligase: “Crystal structure of lysyl-tRNA synthetase from mycobacterium ulcerans complexed with L-lysine and cladosporin”. X-ray diffraction, 2 ligands (LYS, KRS), 20 pockets (best druggability 0.82). MolNFT v1 #143132…
- PDB
- 6AQG
- Type
- protein
- Length
- 1,951 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine--tRNA ligase
- EC
- 6.1.1.6
- UniProt
- A0PV47
- Ligands
- LYS, KRS
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 487 | 37% helix, 27% strand | A0PV47 |
| C | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 490 | 36% helix, 27% strand | A0PV47 |
| D | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 487 | 37% helix, 27% strand | A0PV47 |
Ligands and binding sites
- LYS · Lysine · ligand · 4 copies · chains A, B, C, D
- KRS · cladosporin · ligand · 4 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 9 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 661 | 0.82 | 0.86 | 114 | MPD |
| 2 | 729 | 0.80 | 0.84 | 113 | MPD |
| 3 | 889 | 0.78 | 0.80 | 110 | empty |
| 4 | 735 | 0.77 | 0.82 | 68 | LYS, KRS |
| 5 | 842 | 0.77 | 0.81 | 74 | LYS, KRS |
Interfaces
4 interfaces between chains.
- A–D · 4470 Ų buried · 74 hydrogen bonds · protein-protein
- B–C · 4440 Ų buried · 73 hydrogen bonds · protein-protein
- B–D · 714 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 274 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6AQG · Crystal Structure of Lysyl-tRNA Synthetase from Mycobacterium ulcerans complexed with… · the same entry in another collection · chain D against D, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0PV47
- Elsewhere: RCSB PDB 6AQG · PDBe 6AQG · UniProt A0PV47
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