Research workbench
Crystal structure of tils in a complex with amppnp from aquifex aeolicus.
Analyse Crystal structure of tils in a complex with amppnp from aquifex aeolicus. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2E21
- Type
- protein
- Length
- 1,259 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
- ANP
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA(ILE)-lysidine synthase (EC 6.3.4.-) | protein | 317 | 54% helix, 13% strand | O67728 |
| B, C, D | TRNA(ILE)-lysidine synthase (EC 6.3.4.-) | protein | 314 | 53% helix, 12% strand | O67728 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.82 | 0.84 | 66 | ANP |
| 2 | 778 | 0.82 | 0.85 | 54 | ANP |
| 3 | 968 | 0.78 | 0.81 | 64 | empty |
| 4 | 840 | 0.77 | 0.80 | 51 | empty |
| 5 | 528 | 0.73 | 0.81 | 50 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2013 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 2010 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 775 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 610 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 372 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2E21 · Crystal structure of TilS in a complex with AMPPNP from Aquifex aeolicus. · the same entry in another collection · chain A against A, TM-score 1.00
- O67728 · AlphaFold monomer V2.0 prediction for TRNA(ILE)-lysidine synthase (O67728) · a predicted model of the same protein · chain B 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 2E21 · PDBe 2E21 · UniProt O67728
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