MolNFT v1 · #56968 · protein
Crystal structure of tRNA wybutosine synthesizing enzyme TYW4
2ZW9 · Leucine carboxyl methyltransferase 2: “Crystal structure of tRNA wybutosine synthesizing enzyme TYW4”. X-ray diffraction, 1 ligand (SAM), 16 pockets (best druggability 0.76). MolNFT v1 #56968 on GenesisL1: 3D structure, binding…
- PDB
- 2ZW9
- Type
- protein
- Length
- 1,330 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
- Ligands
- SAM
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine carboxyl methyltransferase 2 (EC 2.1.1.-) | protein | 666 | 26% helix, 29% strand | Q08282 |
| B | Leucine carboxyl methyltransferase 2 (EC 2.1.1.-) | protein | 664 | 26% helix, 29% strand | Q08282 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 254 | 0.76 | 0.89 | 45 | SAM |
| 2 | 425 | 0.75 | 0.85 | 49 | empty |
| 3 | 286 | 0.74 | 0.87 | 53 | SAM |
| 4 | 378 | 0.74 | 0.85 | 53 | empty |
| 5 | 59 | 0.74 | 0.99 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 810 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2ZW9 · 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 0.99
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 2ZW9 · PDBe 2ZW9 · UniProt Q08282
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