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The structure of EANB/Y353F-CYS412-persulfide in tetrahedral intermediate state with ergothioneine
Analyse The structure of EANB/Y353F-CYS412-persulfide in tetrahedral intermediate state… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KW0
- Type
- protein
- Length
- 848 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sulfurtransferase
- UniProt
- B3ECE3
- Ligands
- LW8, MG, CL, BR
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sulfurtransferase | protein | 425 | 32% helix, 17% strand | B3ECE3 |
| B | Sulfurtransferase | protein | 423 | 33% helix, 17% strand | B3ECE3 |
Ligands and binding sites
- LW8 · trimethyl-[(2S)-1-oxidanyl-1-oxidanylidene-3-(2-sulfanylidene-1,3-dihydroimidazol-4-yl)propan-2-yl]azanium · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- BR · Bromide ion · ion · 2 copies · chains A, B
- PGE · Triethylene glycol · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.69 | 0.94 | 21 | LW8 |
| 2 | 83 | 0.67 | 0.92 | 20 | LW8 |
| 3 | 153 | 0.51 | 0.79 | 23 | CL |
| 4 | 144 | 0.51 | 0.79 | 23 | empty |
| 5 | 186 | 0.50 | 0.77 | 31 | BR |
Interfaces
1 interface between chains.
- A–B · 70 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6KW0 · The structure of EanB/Y353F-Cys412-persulfide in tetrahedral intermediate state with… · 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 B3ECE3
- Elsewhere: RCSB PDB 6KW0 · PDBe 6KW0 · UniProt B3ECE3
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