MolNFT v1 · #62781 · protein
Crystal structure of mRNA cap guanine-N7 methyltransferase (rnmt) in complex with sinefungin
3EPP: “Crystal structure of mRNA cap guanine-N7 methyltransferase (rnmt) in complex with sinefungin”. X-ray diffraction, 1 ligand (SFG), 7 pockets (best druggability 0.62). MolNFT v1 #62781 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3EPP
- Type
- protein
- Length
- 533 residues
- Chains
- 2
- 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
- SFG
- Pockets
- 7 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MRNA cap guanine-N7 methyltransferase (EC 2.1.1.56) | protein | 265 | 42% helix, 25% strand | O43148 |
| B | MRNA cap guanine-N7 methyltransferase (EC 2.1.1.56) | protein | 268 | 42% helix, 26% strand | O43148 |
Ligands and binding sites
- SFG · Sinefungin · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.62 | 0.77 | 49 | SFG |
| 2 | 226 | 0.59 | 0.80 | 36 | empty |
| 3 | 343 | 0.57 | 0.76 | 43 | SFG |
| 4 | 152 | 0.45 | 0.75 | 16 | empty |
| 5 | 89 | 0.38 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 570 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3EPP · Crystal structure of mRNA cap guanine-N7 methyltransferase (RNMT) in complex with… · the same entry in another collection · chain A against A, 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
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 3EPP · PDBe 3EPP · UniProt O43148
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