MolNFT v1 · #99242 · protein
Crystal structure wlard, a sugar 3N-formyl transferase in the presence of dtdp and 5-N-formyl-thf
4LXQ: “Crystal structure wlard, a sugar 3N-formyl transferase in the presence of dtdp and 5-N-formyl-thf”. X-ray diffraction, 3 ligands (FON, TYD, CL), 6 pockets (best druggability 0.74). MolNFT v1 #99242 on GenesisL1: 3D structure…
- PDB
- 4LXQ
- 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, TYD, CL
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 26% 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 | 26% 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
- TYD · Thymidine-5'-diphosphate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
- MPO · 3[N-morpholino]propane sulfonic acid · additive · 4 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 | 452 | 0.74 | 0.83 | 44 | FON, TYD |
| 2 | 442 | 0.74 | 0.83 | 45 | FON, TYD |
| 3 | 654 | 0.70 | 0.77 | 49 | empty |
| 4 | 79 | 0.40 | 0.79 | 16 | empty |
| 5 | 82 | 0.40 | 0.78 | 15 | EDO |
Interfaces
1 interface between chains.
- A–B · 1258 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4LXQ · Crystal structure WlaRD, a sugar 3N-formyl transferase in the presence of dTdp and… · 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 A8FMJ3
- Elsewhere: RCSB PDB 4LXQ · PDBe 4LXQ · UniProt A8FMJ3
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