MolNFT v1 · #29975 · protein
Crystal structure of full-legnth A.FULGIDUS RIO1 serine kinase bound to ATP and MN2+ ions.
1ZP9 · RIO1 kinase: “Crystal structure of full-legnth A.FULGIDUS RIO1 serine kinase bound to ATP and MN2+ ions.”. X-ray diffraction, 2 ligands (ATP, MN), 7 pockets (best druggability 0.77). MolNFT v1 #29975 on GenesisL1: 3D structure…
- PDB
- 1ZP9
- Type
- protein
- Length
- 972 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RIO1 kinase
- UniProt
- O28471
- Ligands
- ATP, MN
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RIO1 kinase | protein | 245 | 44% helix, 22% strand | O28471 |
| B | RIO1 kinase | protein | 242 | 43% helix, 23% strand | O28471 |
| C | RIO1 kinase | protein | 241 | 44% helix, 23% strand | O28471 |
| D | RIO1 kinase | protein | 244 | 43% helix, 23% strand | O28471 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 695 | 0.77 | 0.82 | 66 | MN, ATP |
| 2 | 629 | 0.76 | 0.82 | 57 | MN, ATP |
| 3 | 449 | 0.62 | 0.76 | 46 | empty |
| 4 | 261 | 0.62 | 0.80 | 35 | MN, ATP |
| 5 | 254 | 0.61 | 0.80 | 35 | MN, ATP |
Interfaces
3 interfaces between chains.
- A–B · 855 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 840 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 430 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 modified (engineered).
Compared structures
- 1ZP9 · Crystal Structure of full-legnth A.fulgidus Rio1 Serine Kinase bound to ATP and Mn2+ ions. · the same entry in another collection · chain D against D, 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 A against A, TM-score 0.97
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 1ZP9 · PDBe 1ZP9 · UniProt O28471
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