MolNFT v1 · #87822 · protein
X-ray structure of E. COLI ycfd
4CCL · 50S ribosomal protein L16 arginine hydroxylase: “X-ray structure of E. COLI ycfd”. X-ray diffraction, 2 ligands (MN, SO4), 6 pockets (best druggability 0.70). MolNFT v1 #87822 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4CCL
- Type
- protein
- Length
- 743 residues
- Chains
- 2
- 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
- MN, SO4
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 50S ribosomal protein L16 arginine hydroxylase (EC 1.14.11.-) | protein | 371 | 29% helix, 23% strand | P27431 |
| B | 50S ribosomal protein L16 arginine hydroxylase (EC 1.14.11.-) | protein | 372 | 29% helix, 26% strand | P27431 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 9 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.70 | 0.85 | 41 | empty |
| 2 | 379 | 0.68 | 0.81 | 38 | SO4 |
| 3 | 267 | 0.68 | 0.84 | 40 | SO4 |
| 4 | 274 | 0.67 | 0.83 | 38 | MN, SO4 |
| 5 | 69 | 0.44 | 0.81 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 3054 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 modified (engineered).
Compared structures
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 4CCL · PDBe 4CCL · UniProt P27431
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