Research workbench
X-ray structure of the viof N-formyltransferase from providencia alcalifaciens O30 in complex with thf and tdp-QUI4N
Analyse X-ray structure of the viof N-formyltransferase 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
- 4YFY
- Type
- protein
- Length
- 482 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Viof
- UniProt
- M9P0Q2
- Ligands
- 0FX, 1YJ, CL
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Viof | protein | 241 | 34% helix, 27% strand | M9P0Q2 |
Ligands and binding sites
- 0FX · dTDP-4-amino-4,6-dideoxyglucose · ligand · 2 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
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 461 | 0.70 | 0.81 | 45 | 0FX, 1YJ |
| 2 | 468 | 0.70 | 0.81 | 45 | 0FX, 1YJ |
| 3 | 71 | 0.36 | 0.77 | 15 | empty |
| 4 | 84 | 0.36 | 0.76 | 19 | EDO |
Interfaces
1 interface between chains.
- A–B · 1302 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 4YFY · X-ray structure of the Viof N-formyltransferase from Providencia alcalifaciens O30 in… · 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 M9P0Q2
- Elsewhere: RCSB PDB 4YFY · PDBe 4YFY · UniProt M9P0Q2
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