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Structural basis for autoactivation of human MST2 kinase and its regulation by RASSF5
Analyse Structural basis for autoactivation of human MST2 kinase and its regulation by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LGD
- Type
- protein
- Length
- 1,551 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase 3; RAS association domain family member 5, RASSF5
- EC
- 2.7.11.1
- UniProt
- Q13188, Q8WWW0
- Ligands
- ANP, MG, NA, SO4
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 8 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase 3 (EC 2.7.11.1) | protein | 350 | 47% helix, 13% strand | Q13188 |
| B | SERINE/THREONINE-protein kinase 3 (EC 2.7.11.1) | protein | 350 | 45% helix, 14% strand | Q13188 |
| C | SERINE/THREONINE-protein kinase 3 (EC 2.7.11.1) | protein | 349 | 48% helix, 12% strand | Q13188 |
| D | SERINE/THREONINE-protein kinase 3 (EC 2.7.11.1) | protein | 338 | 48% helix, 14% strand | Q13188 |
| E | RAS association domain family member 5, RASSF5 | protein | 47 | 85% helix, 0% strand | Q8WWW0 |
| F | RAS association domain family member 5, RASSF5 | protein | 29 | 83% helix, 0% strand | Q8WWW0 |
| G | RAS association domain family member 5, RASSF5 | protein | 48 | 83% helix, 0% strand | Q8WWW0 |
| H | RAS association domain family member 5, RASSF5 | protein | 40 | 75% helix, 0% strand | Q8WWW0 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 3 copies · chains C, H, D
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, E, C, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 699 | 0.77 | 0.82 | 68 | ANP, MG |
| 2 | 713 | 0.76 | 0.81 | 68 | ANP, MG |
| 3 | 692 | 0.74 | 0.80 | 63 | ANP, MG |
| 4 | 699 | 0.66 | 0.75 | 67 | NA |
| 5 | 283 | 0.63 | 0.80 | 33 | ANP, MG |
Interfaces
13 interfaces between chains.
- C–G · 1477 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 1425 Ų buried · 7 hydrogen bonds · protein-protein
- D–H · 1099 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1016 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 956 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4LGD · Structural Basis for Autoactivation of Human Mst2 Kinase and Its Regulation by RASSF5 · the same entry in another collection · chain H against H, TM-score 1.00
- Q13188 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase 3 (Q13188) · a predicted model of the same protein · chain A against A, TM-score 0.95
- Q8WWW0 · AlphaFold monomer V2.0 prediction for RAS association domain- containing protein 5… · a predicted model of the same protein · chain H against A, TM-score 0.93
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
- Every structure of UniProt Q8WWW0
- Elsewhere: RCSB PDB 4LGD · PDBe 4LGD · UniProt Q13188 · UniProt Q8WWW0
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