MolNFT v1 · #88386 · protein
CNOT1 MIF4G domain - DDX6 complex
4CT4 · CCR4-not transcription complex subunit 1: “CNOT1 MIF4G domain - DDX6 complex”. X-ray diffraction, 2 ligands (MG, CL), 8 pockets (best druggability 0.78). MolNFT v1 #88386 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4CT4
- Type
- protein
- Length
- 1,220 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CCR4-not transcription complex subunit 1; Probable ATP-dependent RNA helicase DDX6
- UniProt
- A5YKK6, P26196
- Ligands
- MG, CL
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CCR4-not transcription complex subunit 1 | protein | 236 | 68% helix, 0% strand | A5YKK6 |
| B | Probable ATP-dependent RNA helicase DDX6 | protein | 378 | 42% helix, 18% strand | P26196 |
| C | CCR4-not transcription complex subunit 1 | protein | 242 | 65% helix, 0% strand | A5YKK6 |
| D | Probable ATP-dependent RNA helicase DDX6 | protein | 364 | 41% helix, 17% strand | P26196 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.78 | 0.80 | 91 | CL |
| 2 | 617 | 0.76 | 0.82 | 73 | empty |
| 3 | 191 | 0.62 | 0.83 | 30 | empty |
| 4 | 203 | 0.59 | 0.80 | 30 | empty |
| 5 | 282 | 0.55 | 0.76 | 41 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1411 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1242 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 35 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4CT4 · CNOT1 MIF4G domain - DDX6 complex · the same entry in another collection · chain D against D, TM-score 1.00
- A5YKK6 · AlphaFold monomer V2.0 prediction for CCR4-not transcription complex subunit 1 (A5YKK6) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P26196 · AlphaFold monomer V2.0 prediction for probable ATP-dependent RNA helicase DDX6 (P26196) · a predicted model of the same protein · chain D against A, TM-score 0.81
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 A5YKK6
- Every structure of UniProt P26196
- Elsewhere: RCSB PDB 4CT4 · PDBe 4CT4 · UniProt A5YKK6 · UniProt P26196
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