Research workbench
Crystal structure of MST2 in complex with xmu-mp-1
Analyse Crystal structure of MST2 in complex with xmu-mp-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DH3
- Type
- protein
- Length
- 574 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase 3
- EC
- 2.7.11.1
- UniProt
- Q13188
- Ligands
- 5BS, CL, SO4
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase 3 (EC 2.7.11.1) | protein | 289 | 43% helix, 19% strand | Q13188 |
| B | SERINE/THREONINE-protein kinase 3 (EC 2.7.11.1) | protein | 285 | 41% helix, 19% strand | Q13188 |
Ligands and binding sites
- 5BS · 4-[(5,10-dimethyl-6-oxo-6,10-dihydro-5H-pyrimido[5,4-b]thieno[3,2-e][1,4]diazepin-2-yl)amino]benzenesulfonamide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.74 | 0.84 | 42 | empty |
| 2 | 262 | 0.69 | 0.84 | 37 | 5BS |
| 3 | 296 | 0.68 | 0.83 | 36 | 5BS |
| 4 | 110 | 0.38 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1020 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
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 Q13188
- Elsewhere: RCSB PDB 5DH3 · PDBe 5DH3 · UniProt Q13188
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