MolNFT v1 · #123240 · protein
Crystal structure of burkholderia glumae toxa Y7F mutant with bound S- adenosylhomocysteine (sah) and toxoflavin
5JDY · Methyl transferase: “Crystal structure of burkholderia glumae toxa Y7F mutant with bound S- adenosylhomocysteine (sah) and…”. X-ray diffraction, 2 ligands (SAH, TOF), 5 pockets (best druggability 0.76). MolNFT v1 #123240 on…
- PDB
- 5JDY
- Type
- protein
- Length
- 482 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl transferase
- UniProt
- Q9LBJ0
- Ligands
- SAH, TOF
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Methyl transferase | protein | 241 | 38% helix, 28% strand | Q9LBJ0 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- TOF · 1,6-dimethylpyrimido[5,4-e][1,2,4]triazine-5,7(1H,6H)-dione · ligand · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.76 | 0.89 | 44 | SAH, TOF |
| 2 | 255 | 0.76 | 0.89 | 46 | SAH, TOF |
| 3 | 251 | 0.74 | 0.88 | 44 | empty |
| 4 | 101 | 0.36 | 0.74 | 18 | empty |
| 5 | 99 | 0.34 | 0.74 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 599 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5JDY · Crystal structure of Burkholderia glumae ToxA Y7F mutant with bound… · 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 Q9LBJ0
- Elsewhere: RCSB PDB 5JDY · PDBe 5JDY · UniProt Q9LBJ0
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