MolNFT v1 · #15289 · protein
Crystal structure of schizosaccharomyces pombe riboflavin kinase reveals a novel ATP and riboflavin binding fold
1N08 · Putative riboflavin kinase: “Crystal structure of schizosaccharomyces pombe riboflavin kinase reveals a novel ATP and riboflavin binding…”. X-ray diffraction, 2 ligands (ADP, ZN), 3 pockets (best druggability 0.73). MolNFT v1 #15289…
- PDB
- 1N08
- Type
- protein
- Length
- 309 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative riboflavin kinase
- EC
- 2.7.1.26
- UniProt
- O74866
- Ligands
- ADP, ZN
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative riboflavin kinase (EC 2.7.1.26) | protein | 154 | 24% helix, 32% strand | O74866 |
| B | Putative riboflavin kinase (EC 2.7.1.26) | protein | 155 | 23% helix, 35% strand | O74866 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 549 | 0.73 | 0.81 | 53 | ZN, ADP |
| 2 | 435 | 0.71 | 0.82 | 54 | empty |
| 3 | 444 | 0.70 | 0.81 | 59 | ZN, ADP |
Interfaces
1 interface between chains.
- A–B · 429 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1N08 · Crystal Structure of Schizosaccharomyces pombe Riboflavin Kinase Reveals a Novel ATP and… · the same entry in another collection · chain A against A, TM-score 1.00
- O74866 · AlphaFold monomer V2.0 prediction for riboflavin kinase (O74866) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 O74866
- Elsewhere: RCSB PDB 1N08 · PDBe 1N08 · UniProt O74866
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