MolNFT v1 · #34398 · protein + RNA
Cocrystal structure of an RNA sulfuration enzyme mnma and tRNA-glu in the pre-reaction state
2DET: “Cocrystal structure of an RNA sulfuration enzyme mnma and tRNA-glu in the pre-reaction state”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.79). MolNFT v1 #34398 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2DET
- Type
- protein + RNA
- Length
- 435 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA; TRNA-specific 2-thiouridylase mnma
- EC
- 2.8.1.-
- UniProt
- P25745
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | TRNA | rna | 70 | — | — |
| A | TRNA-specific 2-thiouridylase mnma (EC 2.8.1.-) | protein | 365 | 28% helix, 24% strand | P25745 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 448 | 0.79 | 0.87 | 55 | SO4 |
| 2 | 777 | 0.74 | 0.80 | 52 | empty |
| 3 | 632 | 0.64 | 0.75 | 27 | empty |
| 4 | 95 | 0.54 | 0.84 | 18 | empty |
| 5 | 133 | 0.47 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- C–A · 1530 Ų buried · 47 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2DET · Cocrystal structure of an RNA sulfuration enzyme MnmA and tRNA-Glu in the pre-reaction… · the same entry in another collection · chain C against C, TM-score 1.00
- P25745 · AlphaFold monomer V2.0 prediction for tRNA-specific 2-thiouridylase mnma (P25745) · a predicted model of the same protein · chain A 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 P25745
- Elsewhere: RCSB PDB 2DET · PDBe 2DET · UniProt P25745
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