Research workbench
Crystal structure of TFB1M and H45 with SAM in homo sapiens
Analyse Crystal structure of TFB1M and H45 with SAM in homo sapiens in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AAX
- Type
- protein + RNA
- Length
- 638 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dimethyladenosine transferase 1, mitochondrial; RNA (28-mer)
- EC
- 2.1.1.-
- UniProt
- Q8WVM0
- Ligands
- SAM
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dimethyladenosine transferase 1, mitochondrial (EC 2.1.1.-) | protein | 290 | 44% helix, 16% strand | Q8WVM0 |
| B, D | RNA (28-mer) | rna | 28 | — | — |
| C | Dimethyladenosine transferase 1, mitochondrial (EC 2.1.1.-) | protein | 292 | 40% helix, 16% strand | Q8WVM0 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains A, C
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 | 325 | 0.74 | 0.86 | 47 | PEG |
| 2 | 198 | 0.60 | 0.81 | 33 | SAM |
| 3 | 187 | 0.59 | 0.81 | 29 | SAM |
| 4 | 387 | 0.54 | 0.74 | 27 | empty |
| 5 | 54 | 0.44 | 0.83 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 889 Ų buried · 22 hydrogen bonds · protein-nucleic
- C–D · 835 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–C · 594 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6AAX · Crystal structure of TFB1M and h45 with SAM in homo sapiens · the same entry in another collection · chain A against A, TM-score 1.00
- Q8WVM0 · AlphaFold monomer V2.0 prediction for dimethyladenosine transferase 1, mitochondrial… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8WVM0
- Elsewhere: RCSB PDB 6AAX · PDBe 6AAX · UniProt Q8WVM0
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