Research workbench
Crystal structure of the zebrafish cap-specific adenosine methyltransferase bound to sah and M7G-capped RNA
Analyse Crystal structure of the zebrafish cap-specific adenosine methyltransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IS0
- Type
- protein + RNA
- Length
- 469 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PDX1 C-terminal-inhibiting factor 1; M7G-capped RNA
- UniProt
- A0A0R4IKJ1
- Ligands
- M7G, SAH
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PDX1 C-terminal-inhibiting factor 1 | protein | 467 | 50% helix, 13% strand | A0A0R4IKJ1 |
| C | M7G-capped RNA | rna | 2 | — | — |
Ligands and binding sites
- M7G · 7N-methyl-8-hydroguanosine-5'-diphosphate · ligand · 2 copies · chains A, C
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.78 | 0.79 | 100 | SAH, EDO |
| 2 | 83 | 0.31 | 0.73 | 16 | M7G |
| 3 | 52 | 0.25 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–C · 157 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nucleotide modification).
Compared structures
- 6IS0 · Crystal structure of the zebrafish cap-specific adenosine methyltransferase bound to SAH… · the same entry in another collection · chain C against C, TM-score 1.00
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 A0A0R4IKJ1
- Elsewhere: RCSB PDB 6IS0 · PDBe 6IS0 · UniProt A0A0R4IKJ1
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