Research workbench
Structure of the SMG1-SMG8-SMG9 complex
Analyse Structure of the SMG1-SMG8-SMG9 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SYT
- Type
- protein
- Length
- 2,582 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SMG1,SERINE/THREONINE-protein kinase SMG1,SMG1, SERINE/THREONINE-protein kinase…
- EC
- 2.7.11.1
- UniProt
- Q96Q15, Q8ND04, Q9H0W8
- Ligands
- IHP, ATP, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 59% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SMG1,SERINE/THREONINE-protein kinase SMG1,SMG1, SERINE/THREONINE-protein kinase SMG1,SMG1,SERINE/THREONINE-protein kinase SMG1,SMG1,SERINE/THREONINE-protein kinase SMG1,SMG1, SERINE/THREONINE-protein kinase SMG1 (EC 2.7.11.1) | protein | 1896 | 65% helix, 2% strand | Q96Q15 |
| B | Protein SMG8 | protein | 377 | 49% helix, 11% strand | Q8ND04 |
| C | Protein SMG9 | protein | 309 | 36% helix, 15% strand | Q9H0W8 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · chains A
- ATP · Adenosine-5'-triphosphate · ligand · chains C
- MG · Magnesium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 868 | 0.85 | 0.87 | 110 | empty |
| 2 | 873 | 0.85 | 0.87 | 97 | empty |
| 3 | 1078 | 0.84 | 0.85 | 92 | empty |
| 4 | 450 | 0.80 | 0.88 | 61 | ATP, MG |
| 5 | 593 | 0.71 | 0.79 | 65 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2379 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1863 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 993 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6SYT · Structure of the SMG1-SMG8-SMG9 complex · the same entry in another collection · chain B against B, TM-score 1.00
- 7PW5 · Human SMG1-8-9 kinase complex with AlphaFold predicted SMG8 C-terminus, bound to a SMG1… · a predicted model of the same protein · chain A against A, TM-score 0.99
- 7PW5 · Human SMG1-8-9 kinase complex with AlphaFold predicted SMG8 C- terminus, bound to a SMG1… · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9H0W8 · AlphaFold monomer V2.0 prediction for protein SMG9 (Q9H0W8) · a predicted model of the same protein · chain C against A, TM-score 0.96
- Q8ND04 · AlphaFold monomer V2.0 prediction for protein SMG8 (Q8ND04) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q96Q15
- Every structure of UniProt Q8ND04
- Every structure of UniProt Q9H0W8
- Elsewhere: RCSB PDB 6SYT · PDBe 6SYT · UniProt Q96Q15 · UniProt Q8ND04 · UniProt Q9H0W8
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