MolNFT v1 · #77407 · protein
Crystal structure of archaeoglobus fulgidus RIO1 kinase bound to toyocamycin.
3RE4 · Rio-type SERINE/THREONINE-protein kinase RIO1: “Crystal structure of archaeoglobus fulgidus RIO1 kinase bound to toyocamycin.”. X-ray diffraction, 1 ligand (TO1), 4 pockets (best druggability 0.80). MolNFT v1 #77407 on GenesisL1: 3D…
- PDB
- 3RE4
- Type
- protein
- Length
- 501 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rio-type SERINE/THREONINE-protein kinase RIO1
- EC
- 2.7.11.1
- UniProt
- O28471
- Ligands
- TO1
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rio-type SERINE/THREONINE-protein kinase RIO1 (EC 2.7.11.1) | protein | 252 | 44% helix, 22% strand | O28471 |
| B | Rio-type SERINE/THREONINE-protein kinase RIO1 (EC 2.7.11.1) | protein | 249 | 44% helix, 22% strand | O28471 |
Ligands and binding sites
- TO1 · 4-amino-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 720 | 0.80 | 0.83 | 64 | TO1 |
| 2 | 311 | 0.63 | 0.79 | 43 | TO1 |
| 3 | 58 | 0.28 | 0.74 | 12 | empty |
| 4 | 60 | 0.28 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 981 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3RE4 · Crystal Structure of Archaeoglobus Fulgidus Rio1 Kinase bound to Toyocamycin. · the same entry in another collection · chain A against A, TM-score 1.00
- O28471 · AlphaFold monomer V2.0 prediction for rio-type SERINE/THREONINE- protein kinase RIO1… · a predicted model of the same protein · chain B against A, TM-score 0.96
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 O28471
- Elsewhere: RCSB PDB 3RE4 · PDBe 3RE4 · UniProt O28471
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