MolNFT v1 · #34399 · protein + RNA
Cocrystal structure of an RNA sulfuration enzyme mnma and tRNA-glu in the adenylated intermediate state
2DEU: “Cocrystal structure of an RNA sulfuration enzyme mnma and tRNA-glu in the adenylated intermediate state”. X-ray diffraction, 2 ligands (AMP, SO4), 16 pockets (best druggability 0.80). MolNFT v1 #34399 on GenesisL1: 3D structure…
- PDB
- 2DEU
- Type
- protein + RNA
- Length
- 876 residues
- Chains
- 4
- 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
- AMP, SO4
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | TRNA | rna | 74 | — | — |
| A, B | TRNA-specific 2-thiouridylase mnma (EC 2.8.1.-) | protein | 364 | 27% helix, 25% strand | P25745 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains C, A, D, B
- SO4 · Sulfate ion · ion · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.80 | 0.89 | 45 | SO4, AMP |
| 2 | 443 | 0.80 | 0.88 | 47 | SO4, AMP |
| 3 | 787 | 0.74 | 0.80 | 40 | empty |
| 4 | 756 | 0.74 | 0.80 | 37 | empty |
| 5 | 605 | 0.63 | 0.75 | 25 | empty |
Interfaces
4 interfaces between chains.
- D–B · 1521 Ų buried · 44 hydrogen bonds · protein-nucleic
- C–A · 1517 Ų buried · 43 hydrogen bonds · protein-nucleic
- C–B · 332 Ų buried · 1 hydrogen bond · protein-nucleic
- D–A · 320 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2DEU · Cocrystal structure of an RNA sulfuration enzyme MnmA and tRNA-Glu in the adenylated… · the same entry in another collection · chain D against D, 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 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 P25745
- Elsewhere: RCSB PDB 2DEU · PDBe 2DEU · UniProt P25745
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