Research workbench
Crystal structure of the saccharomyces cerevisiae sr protein kinsae, SKY1P, complexed with the non-hydrolyzable ATP analogue, AMP-pnp
Analyse Crystal structure of the saccharomyces cerevisiae sr protein kinsae, SKY1P… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Q99
- Type
- protein
- Length
- 718 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sr protein kinsae
- EC
- 2.7.1.-
- UniProt
- Q03656
- Ligands
- ANP, NI, SO4
- Pockets
- 10 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sr protein kinsae (EC 2.7.1.-) | protein | 354 | 41% helix, 19% strand | Q03656 |
| B | Sr protein kinsae (EC 2.7.1.-) | protein | 364 | 38% helix, 18% strand | Q03656 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- MOH · Methanol · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 313 | 0.62 | 0.79 | 31 | ANP |
| 2 | 288 | 0.60 | 0.79 | 32 | ANP |
| 3 | 178 | 0.54 | 0.79 | 23 | empty |
| 4 | 85 | 0.45 | 0.80 | 13 | empty |
| 5 | 104 | 0.43 | 0.78 | 22 | EDO, MOH |
Interfaces
1 interface between chains.
- A–B · 579 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1Q99 · Crystal structure of the Saccharomyces cerevisiae SR protein kinsae, Sky1p, complexed… · the same entry in another collection · chain A against A, TM-score 1.00
- Q03656 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase SKY1 (Q03656) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q03656
- Elsewhere: RCSB PDB 1Q99 · PDBe 1Q99 · UniProt Q03656
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