Research workbench
Crystal structure of a. aeolicus ksga in complex with RNA and sah
Analyse Crystal structure of a. aeolicus ksga in complex with RNA and sah in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FTF
- Type
- protein + RNA
- Length
- 290 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
- Ligands
- SAH, K
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dimethyladenosine transferase (EC 2.1.1.-) | protein | 246 | 32% helix, 20% 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 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 960 | 0.81 | 0.83 | 60 | empty |
| 2 | 204 | 0.78 | 0.92 | 43 | SAH |
| 3 | 72 | 0.29 | 0.73 | 16 | empty |
| 4 | 84 | 0.28 | 0.72 | 11 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1227 Ų buried · 120 hydrogen bonds · nucleic-nucleic
- A–C · 507 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–D · 413 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3FTF · Crystal structure of A. aeolicus KsgA in complex with RNA and SAH · the same entry in another collection · chain C against C, 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 3FTF · PDBe 3FTF · UniProt O67680
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