MolNFT v1 · #185779 · protein + RNA
RNA-bound human ski complex
7QDY · Helicase SKI2W: “RNA-bound human ski complex”. Electron microscopy, 20 pockets (best druggability 0.87). MolNFT v1 #185779 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7QDY
- Type
- protein + RNA
- Length
- 2,997 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Helicase SKI2W; Tetratricopeptide repeat protein 37; Wd repeat-containing protein 61; RNA…
- EC
- 3.6.4.-
- UniProt
- Q15477, Q6PGP7, Q9GZS3
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Helicase SKI2W (EC 3.6.4.-) | protein | 1169 | 39% helix, 10% strand | Q15477 |
| B | Tetratricopeptide repeat protein 37 | protein | 1212 | 72% helix, 1% strand | Q6PGP7 |
| C, D | Wd repeat-containing protein 61 | protein | 305 | 0% helix, 47% strand | Q9GZS3 |
| E | RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') | rna | 6 | — | — |
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 | 801 | 0.87 | 0.90 | 79 | empty |
| 2 | 738 | 0.83 | 0.87 | 52 | empty |
| 3 | 749 | 0.82 | 0.86 | 52 | empty |
| 4 | 1131 | 0.81 | 0.82 | 107 | empty |
| 5 | 1049 | 0.79 | 0.81 | 88 | empty |
Interfaces
6 interfaces between chains.
- A–B · 9122 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 1880 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 980 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 968 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–C · 645 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7QDY · RNA-bound human SKI complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q9GZS3 · AlphaFold monomer V2.0 prediction for wd repeat-containing protein 61 (Q9GZS3) · a predicted model of the same protein · chain C against A, TM-score 0.97
- Q6PGP7 · AlphaFold monomer V2.0 prediction for tetratricopeptide repeat protein 37 (Q6PGP7) · a predicted model of the same protein · chain B against A, TM-score 0.88
- Q15477 · AlphaFold monomer V2.0 prediction for helicase SKI2W (Q15477) · a predicted model of the same protein · chain A against A, TM-score 0.84
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 Q15477
- Every structure of UniProt Q6PGP7
- Every structure of UniProt Q9GZS3
- Elsewhere: RCSB PDB 7QDY · PDBe 7QDY · UniProt Q15477 · UniProt Q6PGP7 · UniProt Q9GZS3
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