Research workbench
Vaccinia methyltransferase VP39 complexed with M7G capped RNA hexamer and S-adenosylhomocysteine
Analyse Vaccinia methyltransferase VP39 complexed with M7G capped RNA hexamer and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1AV6
- Type
- protein + RNA
- Length
- 295 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*GP*AP*AP*AP*AP*A)-3'); Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
- EC
- 2.1.1.57
- UniProt
- P07617
- Ligands
- MGT, SAH
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | RNA (5'-R(*GP*AP*AP*AP*AP*A)-3') | rna | 6 | — | — |
| A | Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase (EC 2.1.1.57) | protein | 289 | 40% helix, 18% strand | P07617 |
Ligands and binding sites
- MGT · 7N-methyl-8-hydroguanosine-5'-triphosphate · ligand · chains B, A
- SAH · S-adenosyl-L-homocysteine · ligand · chains B, A
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 | 222 | 0.54 | 0.78 | 35 | MGT |
| 2 | 103 | 0.50 | 0.82 | 27 | SAH |
| 3 | 107 | 0.49 | 0.81 | 19 | empty |
| 4 | 68 | 0.37 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- B–A · 415 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1AV6 · Vaccinia methyltransferase VP39 complexed with M7G capped RNA hexamer and… · the same entry in another collection · chain B against B, 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 P07617
- Elsewhere: RCSB PDB 1AV6 · PDBe 1AV6 · UniProt P07617
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