MolNFT v1 · #117497 · protein
Crystal structure of mRNA cap guanine-N7 methyltransferase obtained by limited proteolysis
5E9W: “Crystal structure of mRNA cap guanine-N7 methyltransferase obtained by limited proteolysis”. X-ray diffraction, 1 ligand (SAH), 6 pockets (best druggability 0.75). MolNFT v1 #117497 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5E9W
- Type
- protein
- Length
- 1,093 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MRNA cap guanine-N7 methyltransferase
- EC
- 2.1.1.56
- UniProt
- O43148
- Ligands
- SAH
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | MRNA cap guanine-N7 methyltransferase (EC 2.1.1.56) | protein | 273 | 41% helix, 26% strand | O43148 |
| B | MRNA cap guanine-N7 methyltransferase (EC 2.1.1.56) | protein | 273 | 41% helix, 25% strand | O43148 |
| D | MRNA cap guanine-N7 methyltransferase (EC 2.1.1.56) | protein | 274 | 41% helix, 25% strand | O43148 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.75 | 0.79 | 57 | SAH |
| 2 | 1124 | 0.71 | 0.75 | 85 | SAH |
| 3 | 440 | 0.64 | 0.77 | 45 | SAH |
| 4 | 400 | 0.62 | 0.77 | 44 | SAH |
| 5 | 193 | 0.50 | 0.77 | 35 | empty |
Interfaces
2 interfaces between chains.
- B–D · 298 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 227 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5E9W · Crystal structure of mRNA cap guanine-N7 methyltransferase obtained by limited proteolysis · 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 C 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 O43148
- Elsewhere: RCSB PDB 5E9W · PDBe 5E9W · UniProt O43148
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