Research workbench
Crystal structure of mRNA cap guanine-N7 methyltransferase in complex with ram
Analyse Crystal structure of mRNA cap guanine-N7 methyltransferase in complex with ram in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E8J
- Type
- protein
- Length
- 705 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MRNA cap guanine-N7 methyltransferase; Rnmt-activating mini protein
- EC
- 2.1.1.56
- UniProt
- O43148, Q9BTL3
- Ligands
- SAH
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | MRNA cap guanine-N7 methyltransferase (EC 2.1.1.56) | protein | 310 | 38% helix, 25% strand | O43148 |
| C | Rnmt-activating mini protein | protein | 42 | 43% helix, 5% strand | Q9BTL3 |
| D | Rnmt-activating mini protein | protein | 43 | 42% helix, 2% strand | Q9BTL3 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 413 | 0.66 | 0.79 | 44 | SAH |
| 2 | 441 | 0.65 | 0.78 | 41 | GOL, SAH |
| 3 | 465 | 0.63 | 0.76 | 38 | empty |
| 4 | 180 | 0.48 | 0.76 | 25 | empty |
| 5 | 92 | 0.41 | 0.78 | 17 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1844 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1791 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 301 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 181 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5E8J · Crystal structure of mRNA cap guanine-N7 methyltransferase in complex with RAM · the same entry in another collection · chain D against D, TM-score 1.00
- O43148 · AlphaFold monomer V2.0 prediction for mRNA cap guanine-N7 methyltransferase (O43148) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9BTL3 · AlphaFold monomer V2.0 prediction for RNA guanine-N7 methyltransferase activating subunit… · a predicted model of the same protein · chain D against A, TM-score 0.79
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 O43148
- Every structure of UniProt Q9BTL3
- Elsewhere: RCSB PDB 5E8J · PDBe 5E8J · UniProt O43148 · UniProt Q9BTL3
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