MolNFT v1 · #16393 · protein
Crystal structure of staurosporine bound to MAP kap kinase 2
1NXK · MAP kinase-activated protein kinase 2: “Crystal structure of staurosporine bound to MAP kap kinase 2”. X-ray diffraction, 2 ligands (STU, SO4), 18 pockets (best druggability 0.74). MolNFT v1 #16393 on GenesisL1: 3D structure…
- PDB
- 1NXK
- Type
- protein
- Length
- 1,167 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MAP kinase-activated protein kinase 2
- EC
- 2.7.1.-
- UniProt
- P49137
- Ligands
- STU, SO4
- Pockets
- 18 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MAP kinase-activated protein kinase 2 (EC 2.7.1.-) | protein | 290 | 35% helix, 22% strand | P49137 |
| B | MAP kinase-activated protein kinase 2 (EC 2.7.1.-) | protein | 283 | 37% helix, 22% strand | P49137 |
| C | MAP kinase-activated protein kinase 2 (EC 2.7.1.-) | protein | 306 | 39% helix, 21% strand | P49137 |
| D | MAP kinase-activated protein kinase 2 (EC 2.7.1.-) | protein | 288 | 35% helix, 21% strand | P49137 |
Ligands and binding sites
- STU · Staurosporine · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.74 | 0.81 | 80 | empty |
| 2 | 575 | 0.68 | 0.77 | 54 | SO4 |
| 3 | 186 | 0.61 | 0.83 | 26 | STU |
| 4 | 205 | 0.60 | 0.81 | 30 | STU |
| 5 | 197 | 0.60 | 0.81 | 25 | STU |
Interfaces
5 interfaces between chains.
- A–D · 1209 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 858 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 727 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 687 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 225 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 modified (engineered).
Compared structures
- 1NXK · Crystal structure of staurosporine bound to MAP KAP kinase 2 · the same entry in another collection · chain A against A, TM-score 1.00
- P49137 · AlphaFold monomer V2.0 prediction for MAP kinase-activated protein kinase 2 (P49137) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P49137
- Elsewhere: RCSB PDB 1NXK · PDBe 1NXK · UniProt P49137
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.