MolNFT v1 · #109623 · protein
Ergothioneine-biosynthetic sulfoxide synthase egtb in complex with N, N-dimethyl-histidine and gamma-glutamyl-cysteine
4X8D: “Ergothioneine-biosynthetic sulfoxide synthase egtb in complex with N, N-dimethyl-histidine and…”. X-ray diffraction, 6 ligands (3GC, AVI, MG), 10 pockets (best druggability 0.79). MolNFT v1 #109623 on GenesisL1: 3D structure…
- PDB
- 4X8D
- Type
- protein
- Length
- 854 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sulfoxide synthase egtb
- UniProt
- G7CFI3
- Ligands
- 3GC, AVI, MG, MN, CA, CL
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sulfoxide synthase egtb | protein | 428 | 36% helix, 12% strand | G7CFI3 |
| B | Sulfoxide synthase egtb | protein | 426 | 36% helix, 12% strand | G7CFI3 |
Ligands and binding sites
- 3GC · Gamma-glutamylcysteine · ligand · 2 copies · chains A, B
- AVI · N,N-dimethyl-L-histidine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 7 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 12 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 575 | 0.79 | 0.85 | 53 | 3GC, AVI, MN, CL |
| 2 | 587 | 0.79 | 0.85 | 49 | 3GC, AVI, MN, CL |
| 3 | 393 | 0.56 | 0.74 | 55 | empty |
| 4 | 76 | 0.44 | 0.81 | 18 | empty |
| 5 | 72 | 0.42 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 373 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4X8D · Ergothioneine-biosynthetic sulfoxide synthase EgtB in complex with N,N-dimethyl-histidine… · the same entry in another collection · chain A against A, TM-score 1.00
- G7CFI3 · AlphaFold monomer V2.0 prediction for hercynine oxygenase (G7CFI3) · a predicted model of the same protein · chain B 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 G7CFI3
- Elsewhere: RCSB PDB 4X8D · PDBe 4X8D · UniProt G7CFI3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.