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Crystal structure of human METTL1 in complex with sah
Analyse Crystal structure of human METTL1 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
- 7OGJ
- Type
- protein
- Length
- 422 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (guanine-N(7)-)-methyltransferase
- EC
- 2.1.1.33, 2.1.1.-
- UniProt
- Q9UBP6
- Ligands
- SAH, SO4, CL, PO4
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.33, 2.1.1.-) | protein | 210 | 35% helix, 20% strand | Q9UBP6 |
| B | TRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.33, 2.1.1.-) | protein | 212 | 36% helix, 22% strand | Q9UBP6 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- CL · Chloride ion · ion · chains A
- PO4 · Phosphate ion · ion · chains B
- GOL · Glycerol · additive · 5 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.69 | 0.83 | 37 | SAH, SO4 |
| 2 | 492 | 0.67 | 0.78 | 49 | PEG |
| 3 | 296 | 0.62 | 0.79 | 33 | SAH, GOL, CL |
| 4 | 172 | 0.44 | 0.74 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 452 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7OGJ · Crystal structure of human METTL1 in complex with SAH · the same entry in another collection · chain B against B, TM-score 1.00
- Q9UBP6 · AlphaFold monomer V2.0 prediction for tRNA (guanine-N(7)-)-methyltransferase (Q9UBP6) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9UBP6
- Elsewhere: RCSB PDB 7OGJ · PDBe 7OGJ · UniProt Q9UBP6
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