MolNFT v1 · #135998 · protein
Crystal structure of burkholderia thailandensis 1,6- didemethyltoxoflavin-N1-methyltransferase with bound 1,6- didemethyltoxoflavin and S-adenosylhomocysteine
5UFM · Methyltransferase domain protein: “Crystal structure of burkholderia thailandensis 1,6- didemethyltoxoflavin-N1-methyltransferase with bound…”. X-ray diffraction, 3 ligands (SAH, AZ8, SO4), 6 pockets (best druggability 0.75). MolNFT…
- PDB
- 5UFM
- Type
- protein
- Length
- 448 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyltransferase domain protein
- UniProt
- Q2T5S0
- Ligands
- SAH, AZ8, SO4
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyltransferase domain protein | protein | 225 | 36% helix, 31% strand | Q2T5S0 |
| B | Methyltransferase domain protein | protein | 223 | 35% helix, 32% strand | Q2T5S0 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- AZ8 · pyrimido[5,4-e][1,2,4]triazine-5,7(6H,8H)-dione · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 11 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 227 | 0.75 | 0.89 | 49 | SAH, AZ8 |
| 2 | 316 | 0.73 | 0.85 | 57 | SAH, AZ8, SO4 |
| 3 | 146 | 0.47 | 0.77 | 23 | empty |
| 4 | 121 | 0.42 | 0.76 | 24 | empty |
| 5 | 57 | 0.35 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 922 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5UFM · Crystal structure of Burkholderia thailandensis… · 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 Q2T5S0
- Elsewhere: RCSB PDB 5UFM · PDBe 5UFM · UniProt Q2T5S0
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