Research workbench
Crystal structure of lysyl-tRNA synthetase from mycobacterium ulcerans complexed with L-lysine
Analyse Crystal structure of lysyl-tRNA synthetase from mycobacterium ulcerans… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VL1
- Type
- protein
- Length
- 1,941 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
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 486 | 36% helix, 27% strand | A0PV47 |
| B | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 485 | 36% helix, 27% strand | A0PV47 |
| C | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 487 | 37% helix, 26% strand | A0PV47 |
| D | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 483 | 36% helix, 27% strand | A0PV47 |
Ligands and binding sites
- LYS · Lysine · ligand · 4 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 797 | 0.83 | 0.86 | 117 | empty |
| 2 | 1195 | 0.76 | 0.79 | 122 | empty |
| 3 | 294 | 0.76 | 0.88 | 52 | empty |
| 4 | 733 | 0.76 | 0.81 | 61 | PGE, LYS |
| 5 | 1063 | 0.76 | 0.78 | 104 | PGE, LYS |
Interfaces
4 interfaces between chains.
- C–D · 4512 Ų buried · 76 hydrogen bonds · protein-protein
- A–B · 4493 Ų buried · 76 hydrogen bonds · protein-protein
- B–C · 665 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 283 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5VL1 · Crystal Structure of Lysyl-tRNA Synthetase from Mycobacterium ulcerans complexed with… · the same entry in another collection · chain C against C, 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 5VL1 · PDBe 5VL1 · UniProt A0PV47
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