Research workbench
Rhodothermus marinus ycfd-like ribosomal protein L16 arginyl hydroxylase
Analyse Rhodothermus marinus ycfd-like ribosomal protein L16 arginyl hydroxylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CSW
- Type
- protein
- Length
- 776 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cupin 4 family protein
- UniProt
- D0MK34
- Ligands
- UN9, MN
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cupin 4 family protein | protein | 388 | 28% helix, 23% strand | D0MK34 |
Ligands and binding sites
- UN9 · N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine · ligand · 2 copies · chains A
- MN · Manganese (II) ion · metal · chains B
- CIT · Citric acid · additive · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.68 | 0.82 | 38 | empty |
| 2 | 303 | 0.67 | 0.82 | 32 | MN |
| 3 | 167 | 0.51 | 0.78 | 30 | empty |
| 4 | 188 | 0.51 | 0.77 | 33 | empty |
| 5 | 58 | 0.36 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3472 Ų buried · 58 hydrogen bonds · protein-protein
Compared structures
- 4CSW · Rhodothermus marinus YCFD-like ribosomal protein L16 Arginyl hydroxylase · 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
- Elsewhere: RCSB PDB 4CSW · PDBe 4CSW · UniProt D0MK34
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