MolNFT v1 · #98671 · protein
Structural basis for autoactivation of human MST2 kinase and its regulation by RASSF5
4LGD · SERINE/THREONINE-protein kinase 3: “Structural basis for autoactivation of human MST2 kinase and its regulation by RASSF5”. X-ray diffraction, 4 ligands (ANP, MG, NA), 17 pockets (best druggability 0.77). MolNFT v1 #98671 on…
- 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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