Research workbench
Ergothioneine-biosynthetic methyltransferase egtd in complex with chlorohistidine
Analyse Ergothioneine-biosynthetic methyltransferase egtd in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FNR
- Type
- protein
- Length
- 644 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidine N-alpha-methyltransferase
- EC
- 2.1.1.44
- UniProt
- A0A0D6J225
- Ligands
- DYT, MG
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidine N-alpha-methyltransferase (EC 2.1.1.44) | protein | 321 | 41% helix, 27% strand | A0A0D6J225 |
| B | Histidine N-alpha-methyltransferase (EC 2.1.1.44) | protein | 323 | 42% helix, 27% strand | A0A0D6J225 |
Ligands and binding sites
- DYT · (2~{S})-2-chloranyl-3-(1~{H}-imidazol-5-yl)propanoic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 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 | 919 | 0.76 | 0.79 | 74 | GOL, DYT |
| 2 | 1020 | 0.75 | 0.78 | 84 | GOL, DYT |
| 3 | 195 | 0.58 | 0.81 | 33 | PG4 |
| 4 | 77 | 0.37 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 684 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6FNR · Ergothioneine-biosynthetic methyltransferase EgtD in complex with chlorohistidine · 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
- Every structure of UniProt A0A0D6J225
- Elsewhere: RCSB PDB 6FNR · PDBe 6FNR · UniProt A0A0D6J225
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