Research workbench
Crystal structure of a. aeolicus ksga in complex with RNA
Analyse Crystal structure of a. aeolicus ksga in complex with RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FTE
- Type
- protein + RNA
- Length
- 277 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dimethyladenosine transferase; 5'-R(P*AP*AP*CP*CP*GP*UP*AP*GP*GP*GP*GP*AP*AP*CP*CP*UP*GP*C…
- EC
- 2.1.1.-
- UniProt
- O67680
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dimethyladenosine transferase (EC 2.1.1.-) | protein | 233 | 36% helix, 17% strand | O67680 |
| C, D | 5'-R(P*AP*AP*CP*CP*GP*UP*AP*GP*GP*GP*GP*AP*AP*CP*CP*UP*GP*C P*GP*GP*UP*U)-3' | rna | 22 | — | — |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.69 | 0.81 | 41 | empty |
| 2 | 123 | 0.58 | 0.84 | 22 | empty |
| 3 | 190 | 0.57 | 0.80 | 25 | empty |
| 4 | 300 | 0.48 | 0.73 | 20 | empty |
| 5 | 242 | 0.47 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1220 Ų buried · 123 hydrogen bonds · nucleic-nucleic
- A–D · 326 Ų buried · 2 hydrogen bonds · protein-nucleic
- A–C · 118 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3FTE · Crystal structure of A. aeolicus KsgA in complex with RNA · the same entry in another collection · chain A against A, TM-score 1.00
- O67680 · AlphaFold monomer V2.0 prediction for ribosomal RNA small subunit methyltransferase a… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O67680
- Elsewhere: RCSB PDB 3FTE · PDBe 3FTE · UniProt O67680
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