MolNFT v1 · #98750 · protein
Structure of ycfd, a ribosomal oxygenase from escherichia COLI.
4LIU · 50S ribosomal protein L16 arginine hydroxylase: “Structure of ycfd, a ribosomal oxygenase from escherichia COLI.”. X-ray diffraction, 2 ligands (TAM, PO4), 2 pockets (best druggability 0.74). MolNFT v1 #98750 on GenesisL1: 3D…
- PDB
- 4LIU
- Type
- protein
- Length
- 360 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 50S ribosomal protein L16 arginine hydroxylase
- EC
- 1.14.11.-
- UniProt
- P27431
- Ligands
- TAM, PO4
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 50S ribosomal protein L16 arginine hydroxylase (EC 1.14.11.-) | protein | 360 | 29% helix, 25% 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 | 244 | 0.74 | 0.88 | 29 | empty |
| 2 | 303 | 0.67 | 0.83 | 33 | PO4 |
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 4LIU · Structure of YcfD, a Ribosomal oxygenase from Escherichia coli. · 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 4LIU · PDBe 4LIU · UniProt P27431
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