Research workbench
Crystal structure of tRNA wybutosine synthesizing enzyme TYW4
Analyse Crystal structure of tRNA wybutosine synthesizing enzyme TYW4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZZK
- Type
- protein
- Length
- 1,357 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine carboxyl methyltransferase 2
- EC
- 2.1.1.-
- UniProt
- Q08282
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine carboxyl methyltransferase 2 (EC 2.1.1.-) | protein | 680 | 25% helix, 29% strand | Q08282 |
| B | Leucine carboxyl methyltransferase 2 (EC 2.1.1.-) | protein | 677 | 25% helix, 29% strand | Q08282 |
Ligands and binding sites
- CIT · Citric acid · additive · 4 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.75 | 0.99 | 21 | empty |
| 2 | 355 | 0.74 | 0.86 | 48 | empty |
| 3 | 442 | 0.73 | 0.83 | 53 | empty |
| 4 | 58 | 0.72 | 0.98 | 20 | empty |
| 5 | 495 | 0.70 | 0.80 | 45 | CIT |
Interfaces
1 interface between chains.
- A–B · 760 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2ZZK · Crystal structure of tRNA wybutosine synthesizing enzyme TYW4 · the same entry in another collection · chain A against A, TM-score 1.00
- Q08282 · AlphaFold monomer V2.0 prediction for tRNA wybutosine-synthesizing protein 4 (Q08282) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q08282
- Elsewhere: RCSB PDB 2ZZK · PDBe 2ZZK · UniProt Q08282
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