MolNFT v1 · #99246 · protein
Dtdp-FUC3N and 5-N-formyl-thf
4LXU · Wlard, a sugar 3N-formyl transferase: “Dtdp-FUC3N and 5-N-formyl-thf”. X-ray diffraction, 4 ligands (FON, T3F, CL), 6 pockets (best druggability 0.73). MolNFT v1 #99246 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4LXU
- Type
- protein
- Length
- 547 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wlard, a sugar 3N-formyl transferase
- UniProt
- A8FMJ3
- Ligands
- FON, T3F, CL, SO4
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wlard, a sugar 3N-formyl transferase | protein | 273 | 26% helix, 27% strand | A8FMJ3 |
| B | Wlard, a sugar 3N-formyl transferase | protein | 274 | 25% helix, 27% strand | A8FMJ3 |
Ligands and binding sites
- FON · N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid · ligand · 2 copies · chains A, B
- 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 · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
- MPO · 3[N-morpholino]propane sulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.73 | 0.83 | 45 | FON, T3F, CL |
| 2 | 386 | 0.73 | 0.84 | 45 | FON, T3F |
| 3 | 667 | 0.71 | 0.78 | 49 | EDO |
| 4 | 94 | 0.45 | 0.80 | 15 | EDO |
| 5 | 82 | 0.41 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1310 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4LXU · dTdp-Fuc3N and 5-N-Formyl-THF · the same entry in another collection · chain B against B, 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 A8FMJ3
- Elsewhere: RCSB PDB 4LXU · PDBe 4LXU · UniProt A8FMJ3
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