Research workbench
Crystal structure of human MYT1 kinase domain bounded with rp-6306
Analyse Crystal structure of human MYT1 kinase domain bounded with rp-6306 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8D6E
- Type
- protein
- Length
- 559 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Membrane-associated tyrosine- and threonine-specific CDC2- inhibitory kinase
- EC
- 2.7.11.1
- UniProt
- Q99640
- Ligands
- QGI, SO4
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Membrane-associated tyrosine- and threonine-specific CDC2- inhibitory kinase (EC 2.7.11.1) | protein | 281 | 37% helix, 19% strand | Q99640 |
| A | Membrane-associated tyrosine- and threonine-specific CDC2- inhibitory kinase (EC 2.7.11.1) | protein | 278 | 37% helix, 19% strand | Q99640 |
Ligands and binding sites
- QGI · (1P)-2-amino-1-(3-hydroxy-2,6-dimethylphenyl)-5,6-dimethyl-1H-pyrrolo[2,3-b]pyridine-3-carboxamide · ligand · 2 copies · chains B, A
- SO4 · Sulfate ion · ion · 2 copies · chains B, A
- EDO · 1,2-ethanediol · additive · 12 copies · chains B, A
- GOL · Glycerol · additive · 3 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1033 | 0.80 | 0.82 | 117 | QGI, EDO |
| 2 | 126 | 0.42 | 0.75 | 21 | empty |
| 3 | 89 | 0.38 | 0.76 | 20 | empty |
| 4 | 60 | 0.37 | 0.80 | 12 | empty |
| 5 | 76 | 0.36 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- B–A · 338 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 8D6E · Crystal Structure of Human Myt1 Kinase domain Bounded with RP-6306 · the same entry in another collection · chain B against B, TM-score 1.00
- Q99640 · AlphaFold monomer V2.0 prediction for membrane-associated tyrosine- and… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q99640
- Elsewhere: RCSB PDB 8D6E · PDBe 8D6E · UniProt Q99640
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.