Research workbench
Crystal structure of Escherichia coli ribosomal oxygenase YcfD
Analyse Crystal structure of Escherichia coli ribosomal oxygenase YcfD in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NUB
- Type
- protein
- Length
- 361 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Escherichia coli
- Molecule
- 50S ribosomal protein L16 arginine hydroxylase
- EC
- 1.14.11.-
- UniProt
- P27431
- Ligands
- FE
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · resolution 2.7 · 1 distinct chain · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 50S ribosomal protein L16 arginine hydroxylase (EC 1.14.11.-) | protein | 361 | 29% helix, 24% strand | P27431 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.70 | 0.86 | 30 | empty |
| 2 | 305 | 0.65 | 0.81 | 40 | FE |
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 4NUB · Crystal structure of escherichia COLI ribosomal oxygenase ycfd · the same entry in another collection · chain A against A, TM-score 1.00
- P27431 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L16 3-hydroxylase (P27431) · a predicted model of the same protein · 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 P27431
- Elsewhere: RCSB PDB 4NUB · PDBe 4NUB · UniProt P27431
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