MolNFT v1 · #88430 · protein
Rhodothermus marinus ycfd-like ribosomal protein L16 arginyl hydroxylase in complex substrate fragment
4CUG · Cupin 4 family protein: “Rhodothermus marinus ycfd-like ribosomal protein L16 arginyl hydroxylase in complex substrate fragment”. X-ray diffraction, 3 ligands (OGA, MN, PO4), 10 pockets (best druggability 0.76). MolNFT v1 #88430 on…
- PDB
- 4CUG
- Type
- protein
- Length
- 790 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cupin 4 family protein; 50S ribosomal protein L16
- UniProt
- D0MK34, D0MGW1
- Ligands
- OGA, MN, PO4
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cupin 4 family protein | protein | 388 | 27% helix, 23% strand | D0MK34 |
| B | Cupin 4 family protein | protein | 385 | 28% helix, 24% strand | D0MK34 |
| E | 50S ribosomal protein L16 | protein | 8 | 0% helix, 0% strand | D0MGW1 |
| F | 50S ribosomal protein L16 | protein | 9 | 0% helix, 0% strand | D0MGW1 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 2 copies · chains A, E, B, F
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A, E
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.76 | 0.99 | 18 | MN, OGA |
| 2 | 63 | 0.73 | 0.99 | 20 | OGA |
| 3 | 209 | 0.57 | 0.79 | 19 | MPD |
| 4 | 229 | 0.54 | 0.78 | 30 | MPD, PO4 |
| 5 | 150 | 0.49 | 0.78 | 30 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3405 Ų buried · 63 hydrogen bonds · protein-protein
- B–F · 643 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 606 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 14 Ų buried · 0 hydrogen bonds · protein-protein
- B–E · 12 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4CUG · Rhodothermus marinus YCFD-like ribosomal protein L16 Arginyl hydroxylase in complex… · 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 D0MK34
- Every structure of UniProt D0MGW1
- Elsewhere: RCSB PDB 4CUG · PDBe 4CUG · UniProt D0MK34 · UniProt D0MGW1
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