Research workbench
Ergothioneine-biosynthetic methyltransferase egtd, apo form
Analyse Ergothioneine-biosynthetic methyltransferase egtd, apo form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PIM
- Type
- protein
- Length
- 645 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
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidine-specific methyltransferase egtd (EC 2.1.1.44) | protein | 322 | 43% helix, 26% strand | A0R5M8 |
| B | Histidine-specific methyltransferase egtd (EC 2.1.1.44) | protein | 323 | 42% helix, 27% strand | A0R5M8 |
Ligands and binding sites
- ACT · Acetate ion · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.77 | 0.80 | 84 | ACT |
| 2 | 981 | 0.74 | 0.77 | 73 | ACT |
| 3 | 96 | 0.45 | 0.80 | 18 | empty |
| 4 | 95 | 0.41 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 710 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 4PIM · Ergothioneine-biosynthetic methyltransferase EgtD, apo form · 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 B 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 4PIM · PDBe 4PIM · UniProt A0R5M8
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