MolNFT v1 · #109624 · protein
Ergothioneine-biosynthetic sulfoxide synthase egtb in complex with N, N,N-trimethyl-histidine
4X8E: “Ergothioneine-biosynthetic sulfoxide synthase egtb in complex with N, N,N-trimethyl-histidine”. X-ray diffraction, 5 ligands (AVJ, FE, CA), 10 pockets (best druggability 0.80). MolNFT v1 #109624 on GenesisL1: 3D structure, binding…
- PDB
- 4X8E
- 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
- AVJ, FE, CA, MG, CL
- Pockets
- 10 · best druggability 0.80
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
- AVJ · N,N,N-trimethyl-histidine · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 7 copies · chains A, B
- GOL · Glycerol · additive · 12 copies · chains A, B
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 | 569 | 0.80 | 0.86 | 53 | AVJ, GOL, CL, FE |
| 2 | 574 | 0.79 | 0.84 | 53 | AVJ, CL, FE |
| 3 | 370 | 0.54 | 0.73 | 54 | empty |
| 4 | 77 | 0.45 | 0.81 | 20 | empty |
| 5 | 77 | 0.44 | 0.81 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 360 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 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 4X8E · PDBe 4X8E · UniProt G7CFI3
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