MolNFT v1 · #128243 · protein
SMG8-SMG9 complex
5NKM · Protein smg-8: “SMG8-SMG9 complex”. X-ray diffraction, 20 pockets (best druggability 0.83). MolNFT v1 #128243 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5NKM
- Type
- protein
- Length
- 1,824 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein smg-8; Protein smg-9
- UniProt
- O62301, Q9XWJ1
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein smg-8 | protein | 345 | 52% helix, 11% strand | O62301 |
| B | Protein smg-9 | protein | 260 | 40% helix, 17% strand | Q9XWJ1 |
| C | Protein smg-8 | protein | 347 | 52% helix, 11% strand | O62301 |
| D | Protein smg-9 | protein | 263 | 39% helix, 17% strand | Q9XWJ1 |
| E | Protein smg-8 | protein | 351 | 52% helix, 12% strand | O62301 |
| F | Protein smg-9 | protein | 258 | 40% helix, 17% strand | Q9XWJ1 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C, D, E
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains C, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1012 | 0.83 | 0.84 | 110 | TRS |
| 2 | 1088 | 0.81 | 0.82 | 106 | EDO |
| 3 | 597 | 0.79 | 0.84 | 73 | TRS |
| 4 | 431 | 0.71 | 0.82 | 46 | EDO |
| 5 | 51 | 0.68 | 0.96 | 19 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1925 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1816 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1757 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 938 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 810 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 modified (engineered).
Compared structures
- 5NKM · SMG8-SMG9 complex · the same entry in another collection · chain F against F, TM-score 1.00
- O62301 · AlphaFold monomer V2.0 prediction for protein smg-8 (O62301) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9XWJ1 · AlphaFold monomer V2.0 prediction for protein smg-9 (Q9XWJ1) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 O62301
- Every structure of UniProt Q9XWJ1
- Elsewhere: RCSB PDB 5NKM · PDBe 5NKM · UniProt O62301 · UniProt Q9XWJ1
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