MolNFT v1 · #103502 · protein
Ergothioneine-biosynthetic methyltransferase egtd in complex with N,N- dimethylhistidine and sah
4PIO · Histidine-specific methyltransferase egtd: “Ergothioneine-biosynthetic methyltransferase egtd in complex with N,N- dimethylhistidine and sah”. X-ray diffraction, 4 ligands (SAH, AVI, MG), 5 pockets (best druggability 0.77). MolNFT…
- PDB
- 4PIO
- Type
- protein
- Length
- 625 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidine-specific methyltransferase egtd
- EC
- 2.1.1.44
- UniProt
- A0R5M8
- Ligands
- SAH, AVI, MG, CL
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidine-specific methyltransferase egtd (EC 2.1.1.44) | protein | 307 | 42% helix, 26% strand | A0R5M8 |
| B | Histidine-specific methyltransferase egtd (EC 2.1.1.44) | protein | 318 | 42% helix, 26% strand | A0R5M8 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- AVI · N,N-dimethyl-L-histidine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.77 | 0.86 | 60 | SAH, AVI |
| 2 | 354 | 0.76 | 0.87 | 48 | SAH |
| 3 | 581 | 0.65 | 0.76 | 50 | empty |
| 4 | 194 | 0.49 | 0.76 | 26 | empty |
| 5 | 109 | 0.46 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 323 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 4PIO · Ergothioneine-biosynthetic methyltransferase EgtD in complex with N,N-dimethylhistidine… · the same entry in another collection · chain A against A, TM-score 1.00
- A0R5M8 · AlphaFold monomer V2.0 prediction for histidine N-alpha- methyltransferase (A0R5M8) · 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 A0R5M8
- Elsewhere: RCSB PDB 4PIO · PDBe 4PIO · UniProt A0R5M8
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