Research workbench
Drosophila NOT4 cbm peptide bound to human CAF40
Analyse Drosophila NOT4 cbm peptide bound to human CAF40 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HOM
- Type
- protein
- Length
- 595 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CCR4-not transcription complex subunit 9; CCR4-not transcription complex subunit 4…
- UniProt
- Q92600, M9PCL9
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.54
Structure
x-ray diffraction · 4 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CCR4-not transcription complex subunit 9 | protein | 273 | 75% helix, 0% strand | Q92600 |
| B | CCR4-not transcription complex subunit 4, isoform L | protein | 25 | 56% helix, 0% strand | M9PCL9 |
| C | CCR4-not transcription complex subunit 9 | protein | 271 | 75% helix, 0% strand | Q92600 |
| D | CCR4-not transcription complex subunit 4, isoform L | protein | 26 | 54% helix, 0% strand | M9PCL9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, C
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.54 | 0.81 | 21 | empty |
| 2 | 158 | 0.48 | 0.77 | 25 | empty |
| 3 | 137 | 0.44 | 0.76 | 16 | TRS |
| 4 | 97 | 0.41 | 0.77 | 19 | empty |
| 5 | 105 | 0.39 | 0.76 | 24 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1163 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1008 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 992 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6HOM · Drosophila NOT4 CBM peptide bound to human CAF40 · the same entry in another collection · chain A against A, TM-score 1.00
- Q92600 · AlphaFold monomer V2.0 prediction for CCR4-not transcription complex subunit 9 (Q92600) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q92600
- Every structure of UniProt M9PCL9
- Elsewhere: RCSB PDB 6HOM · PDBe 6HOM · UniProt Q92600 · UniProt M9PCL9
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