MolNFT v1 · #117719 · protein
Crystal structure of the S-methyltransferase tmta
5EGP · UBIE/COQ5 family methyltransferase, putative: “Crystal structure of the S-methyltransferase tmta”. X-ray diffraction, 2 ligands (SAH, SO4), 3 pockets (best druggability 0.89). MolNFT v1 #117719 on GenesisL1: 3D structure, binding…
- PDB
- 5EGP
- Type
- protein
- Length
- 563 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UBIE/COQ5 family methyltransferase, putative
- Ligands
- SAH, SO4
- Pockets
- 3 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UBIE/COQ5 family methyltransferase, putative | protein | 282 | 48% helix, 24% strand | — |
| B | UBIE/COQ5 family methyltransferase, putative | protein | 281 | 49% helix, 25% strand | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- ACT · Acetate ion · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.89 | 0.90 | 110 | SAH, SO4, ACT |
| 2 | 189 | 0.49 | 0.76 | 31 | empty |
| 3 | 55 | 0.28 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1407 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5EGP · Crystal structure of the S-methyltransferase TmtA · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 5EGP · PDBe 5EGP
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