Research workbench
X-ray structure of the N-formyltransferase qdtf from providencia alcalifaciens
Analyse X-ray structure of the N-formyltransferase qdtf from providencia alcalifaciens in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XD0
- Type
- protein
- Length
- 397 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tdp-3-aminoquinovose-N-formyltransferase
- EC
- 2.1.2.9
- UniProt
- F8RC03
- Ligands
- T3F, FON, NA, K, CL
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tdp-3-aminoquinovose-N-formyltransferase (EC 2.1.2.9) | protein | 397 | 37% helix, 18% strand | F8RC03 |
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 · 2 copies · chains A
- 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 · chains A
- NA · Sodium ion · metal · 3 copies · chains A
- K · Potassium ion · metal · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.74 | 0.82 | 46 | FON, T3F |
| 2 | 434 | 0.60 | 0.76 | 41 | empty |
| 3 | 92 | 0.38 | 0.76 | 16 | empty |
| 4 | 67 | 0.37 | 0.78 | 13 | empty |
| 5 | 54 | 0.29 | 0.74 | 13 | T3F |
Compared structures
- 4XD0 · X-ray structure of the N-formyltransferase QdtF from Providencia alcalifaciens · 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 F8RC03
- Elsewhere: RCSB PDB 4XD0 · PDBe 4XD0 · UniProt F8RC03
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