MolNFT v2 · #173212 · protein
Structure of SMG1-8-9 kinase complex bound to UPF1-LSQ
6Z3R · Serine/threonine-protein kinase…: “Structure of SMG1-8-9 kinase complex bound to UPF1-LSQ”. Electron microscopy at 2.97, 4 ligands (ANP, IHP, ATP), 20 pockets (best druggability 0.88). MolNFT v2 #173212 on GenesisL1: 3D structure…
- PDB
- 6Z3R
- Type
- protein
- Length
- 2,636 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.97
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase…
- EC
- 2.7.11.1, 3.6.4.-
- UniProt
- Q96Q15, Q8ND04, Q9H0W8, Q92900
- Ligands
- ANP, IHP, ATP, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · resolution 2.97 · 4 distinct chains · 57% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1 (EC 2.7.11.1) | protein | 1943 | 62% helix, 2% strand | Q96Q15 |
| B | Protein SMG8 | protein | 376 | 48% helix, 11% strand | Q8ND04 |
| C | Protein SMG9 | protein | 310 | 36% helix, 15% strand | Q9H0W8 |
| E | Regulator of nonsense transcripts 1 (EC 3.6.4.-) | protein | 7 | 0% helix, 0% strand | Q92900 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- 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 | 1066 | 0.88 | 0.89 | 129 | ATP, MG |
| 2 | 935 | 0.85 | 0.87 | 104 | empty |
| 3 | 1092 | 0.81 | 0.82 | 97 | empty |
| 4 | 986 | 0.80 | 0.81 | 105 | empty |
| 5 | 1093 | 0.77 | 0.79 | 95 | empty |
Interfaces
4 interfaces between chains.
- B–C · 2316 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 2022 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 994 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 385 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6Z3R · Structure of SMG1-8-9 kinase complex bound to UPF1-lsq · 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 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 1.00
- 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
- Every structure of UniProt Q92900
- Elsewhere: RCSB PDB 6Z3R · PDBe 6Z3R · UniProt Q96Q15 · UniProt Q8ND04 · UniProt Q9H0W8 · UniProt Q92900
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