MolNFT v1 · #41091 · protein
SKY1P bound to NPL3P-derived substrate peptide
2JD5 · SERINE/THREONINE-protein kinase SKY1: “SKY1P bound to NPL3P-derived substrate peptide”. X-ray diffraction, 2 ligands (MG, SO4), 10 pockets (best druggability 0.62). MolNFT v1 #41091 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2JD5
- Type
- protein
- Length
- 718 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase SKY1; Nucleolar protein 3
- EC
- 2.7.11.1
- UniProt
- Q03656, Q01560
- Ligands
- MG, SO4
- Pockets
- 10 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase SKY1 (EC 2.7.11.1) | protein | 353 | 38% helix, 19% strand | Q03656 |
| B | SERINE/THREONINE-protein kinase SKY1 (EC 2.7.11.1) | protein | 360 | 37% helix, 18% strand | Q03656 |
| C | Nucleolar protein 3 | protein | 5 | 0% helix, 0% strand | Q01560 |
Ligands and binding sites
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 | 284 | 0.62 | 0.80 | 31 | MG |
| 2 | 279 | 0.59 | 0.78 | 30 | MG |
| 3 | 75 | 0.54 | 0.86 | 22 | empty |
| 4 | 79 | 0.43 | 0.79 | 14 | empty |
| 5 | 78 | 0.37 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 598 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 402 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 110 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2JD5 · Sky1p bound to Npl3p-derived substrate peptide · 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 0.98
- Q01560 · AlphaFold monomer V2.0 prediction for nucleolar protein 3 (Q01560) · a predicted model of the same protein · chain C against A, TM-score 0.73
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
- Every structure of UniProt Q01560
- Elsewhere: RCSB PDB 2JD5 · PDBe 2JD5 · UniProt Q03656 · UniProt Q01560
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