Research workbench
Cocrystal structure of an RNA sulfuration enzyme mnma and tRNA-glu in the initial tRNA binding state
Analyse Cocrystal structure of an RNA sulfuration enzyme mnma and tRNA-glu in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DER
- Type
- protein + RNA
- Length
- 852 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
- SO4, PO4
- Pockets
- 19 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | TRNA | rna | 74 | — | — |
| D | TRNA | rna | 71 | — | — |
| A | TRNA-specific 2-thiouridylase mnma (EC 2.8.1.-) | protein | 348 | 27% helix, 30% strand | P25745 |
| B | TRNA-specific 2-thiouridylase mnma (EC 2.8.1.-) | protein | 359 | 27% helix, 30% strand | P25745 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains D, B, C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 923 | 0.78 | 0.80 | 67 | empty |
| 2 | 97 | 0.74 | 0.96 | 20 | empty |
| 3 | 794 | 0.70 | 0.76 | 49 | PO4 |
| 4 | 483 | 0.69 | 0.80 | 50 | PO4 |
| 5 | 588 | 0.67 | 0.78 | 37 | empty |
Interfaces
4 interfaces between chains.
- C–A · 1332 Ų buried · 31 hydrogen bonds · protein-nucleic
- D–B · 1213 Ų buried · 35 hydrogen bonds · protein-nucleic
- A–B · 924 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 149 Ų buried · 4 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2DER · Cocrystal structure of an RNA sulfuration enzyme MnmA and tRNA-Glu in the initial tRNA… · 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 2DER · PDBe 2DER · UniProt P25745
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