MolNFT v1 · #127979 · protein
Crystal structure of the CBK1-MOB2 kinase-coactivator complex with an SSD1 peptide
5NCL · SERINE/THREONINE-protein kinase CBK1: “Crystal structure of the CBK1-MOB2 kinase-coactivator complex with an SSD1 peptide”. X-ray diffraction, 1 ligand (ANP), 10 pockets (best druggability 0.81). MolNFT v1 #127979 on GenesisL1: 3D…
- PDB
- 5NCL
- Type
- protein
- Length
- 604 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase CBK1; CBK1 kinase activator protein MOB2; Protein SSD1
- EC
- 2.7.11.1
- UniProt
- P53894, P43563, P24276
- Ligands
- ANP
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase CBK1 (EC 2.7.11.1) | protein | 418 | 37% helix, 10% strand | P53894 |
| B | CBK1 kinase activator protein MOB2 | protein | 181 | 54% helix, 0% strand | P43563 |
| D | Protein SSD1 | protein | 5 | 0% helix, 0% strand | P24276 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1121 | 0.81 | 0.82 | 106 | ANP |
| 2 | 253 | 0.67 | 0.84 | 27 | empty |
| 3 | 177 | 0.61 | 0.83 | 25 | empty |
| 4 | 224 | 0.60 | 0.81 | 31 | empty |
| 5 | 75 | 0.56 | 0.87 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1891 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 330 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5NCL · Crystal structure of the Cbk1-Mob2 kinase-coactivator complex with an SSD1 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P43563 · AlphaFold monomer V2.0 prediction for CBK1 kinase activator protein MOB2 (P43563) · a predicted model of the same protein · chain B against A, TM-score 0.95
- P53894 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase CBK1 (P53894) · a predicted model of the same protein · chain A against A, TM-score 0.92
- P24276 · AlphaFold monomer V2.0 prediction for protein SSD1 (P24276) · a predicted model of the same protein · chain D against A, TM-score 0.82
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 P53894
- Every structure of UniProt P43563
- Every structure of UniProt P24276
- Elsewhere: RCSB PDB 5NCL · PDBe 5NCL · UniProt P53894 · UniProt P43563 · UniProt P24276
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