MolNFT v1 · #35335 · protein
Crystal structure of aquifex aeolicus tils in a complex with ATP, magnesium ion, and L-lysine
2E89 · TRNA(ILE)-lysidine synthase: “Crystal structure of aquifex aeolicus tils in a complex with ATP, magnesium ion, and L-lysine”. X-ray diffraction, 3 ligands (ATP, LYS, MG), 14 pockets (best druggability 0.79). MolNFT v1 #35335 on…
- PDB
- 2E89
- Type
- protein
- Length
- 1,258 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA(ILE)-lysidine synthase
- EC
- 6.3.4.-
- UniProt
- O67728
- Ligands
- ATP, LYS, MG
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA(ILE)-lysidine synthase (EC 6.3.4.-) | protein | 317 | 51% helix, 14% strand | O67728 |
| B, C | TRNA(ILE)-lysidine synthase (EC 6.3.4.-) | protein | 314 | 52% helix, 13% strand | O67728 |
| D | TRNA(ILE)-lysidine synthase (EC 6.3.4.-) | protein | 313 | 54% helix, 10% strand | O67728 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- LYS · Lysine · ligand · chains B
- MG · Magnesium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 864 | 0.79 | 0.82 | 53 | MG, ATP |
| 2 | 1057 | 0.79 | 0.81 | 65 | ATP |
| 3 | 915 | 0.78 | 0.81 | 56 | ATP |
| 4 | 915 | 0.77 | 0.80 | 58 | ATP |
| 5 | 126 | 0.58 | 0.84 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2013 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1990 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 371 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2E89 · Crystal structure of Aquifex aeolicus TilS in a complex with ATP, Magnesium ion, and… · the same entry in another collection · chain D against D, TM-score 1.00
- O67728 · AlphaFold monomer V2.0 prediction for TRNA(ILE)-lysidine synthase (O67728) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 O67728
- Elsewhere: RCSB PDB 2E89 · PDBe 2E89 · UniProt O67728
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