MolNFT v1 · #136098 · protein
X-ray structure of the fdtf N-formyltransferase from salmonella enterica O60 in complex with tdp-FUC3N and tetrahydrofolate
5UIL: “X-ray structure of the fdtf N-formyltransferase from salmonella enterica O60 in complex with tdp-FUC3N and…”. X-ray diffraction, 3 ligands (T3F, 1YJ, NA), 10 pockets (best druggability 0.74). MolNFT v1 #136098 on GenesisL1: 3D…
- PDB
- 5UIL
- Type
- protein
- Length
- 796 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formyltransferase
- UniProt
- U3GK13
- Ligands
- T3F, 1YJ, NA
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formyltransferase | protein | 398 | 36% helix, 19% strand | U3GK13 |
| B | Formyltransferase | protein | 398 | 36% helix, 18% strand | U3GK13 |
Ligands and binding sites
- T3F · (3R,4S,5R,6R)-4-amino-3,5-dihydroxy-6-methyloxan-2-yl][hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate · ligand · 4 copies · chains A, B
- 1YJ · N-[4-({[(6R)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 4 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 559 | 0.74 | 0.81 | 54 | 1YJ, T3F |
| 2 | 765 | 0.73 | 0.78 | 52 | empty |
| 3 | 454 | 0.72 | 0.82 | 44 | 1YJ, T3F |
| 4 | 299 | 0.57 | 0.77 | 32 | empty |
| 5 | 285 | 0.56 | 0.76 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 1412 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 5UIL · X-ray structure of the FdtF N-formyltransferase from Salmonella enterica O60 in complex… · 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 U3GK13
- Elsewhere: RCSB PDB 5UIL · PDBe 5UIL · UniProt U3GK13
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