Research workbench
Crystal structure of mRNA cap guanine-N7 methyltransferase in complex with sah
Analyse Crystal structure of mRNA cap guanine-N7 methyltransferase in complex with sah in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BGV
- Type
- protein
- Length
- 1,078 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
- 10 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MRNA cap guanine-N7 methyltransferase (EC 2.1.1.56) | protein | 269 | 40% helix, 26% strand | O43148 |
| B | MRNA cap guanine-N7 methyltransferase (EC 2.1.1.56) | protein | 271 | 41% helix, 26% strand | O43148 |
| C | MRNA cap guanine-N7 methyltransferase (EC 2.1.1.56) | protein | 270 | 40% helix, 26% strand | O43148 |
| D | MRNA cap guanine-N7 methyltransferase (EC 2.1.1.56) | protein | 268 | 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
10 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 | 0.72 | 0.77 | 64 | SAH |
| 2 | 714 | 0.69 | 0.76 | 60 | SAH |
| 3 | 437 | 0.62 | 0.77 | 46 | SAH |
| 4 | 421 | 0.62 | 0.77 | 52 | SAH |
| 5 | 201 | 0.52 | 0.77 | 21 | empty |
Interfaces
2 interfaces between chains.
- B–D · 243 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 185 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3BGV · Crystal structure of mRNA cap guanine-N7 methyltransferase in complex with SAH · 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 0.98
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 3BGV · PDBe 3BGV · UniProt O43148
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