Research workbench
Drosophila Bag-of-marbles CBM peptide bound to human CAF40-CNOT1
Analyse Drosophila Bag-of-marbles CBM peptide bound to human CAF40-CNOT1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ONA
- Type
- protein
- Length
- 1,057 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- CCR4-NOT transcription complex subunit 1; CCR4-NOT transcription complex subunit 9…
- UniProt
- A5YKK6, Q92600, P22745
- Ligands
- SO4, CL
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.7 · 6 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CCR4-NOT transcription complex subunit 1 | protein | 236 | 72% helix, 0% strand | A5YKK6 |
| B | CCR4-NOT transcription complex subunit 9 | protein | 273 | 75% helix, 0% strand | Q92600 |
| C | Protein bag-of-marbles | protein | 22 | 91% helix, 0% strand | P22745 |
| D | CCR4-NOT transcription complex subunit 1 | protein | 234 | 73% helix, 0% strand | A5YKK6 |
| E | CCR4-NOT transcription complex subunit 9 | protein | 271 | 75% helix, 0% strand | Q92600 |
| F | Protein bag-of-marbles | protein | 21 | 90% helix, 0% strand | P22745 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, D, C, E
- CL · Chloride ion · ion · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.82 | 0.86 | 87 | SO4 |
| 2 | 306 | 0.74 | 0.86 | 42 | empty |
| 3 | 154 | 0.65 | 0.86 | 33 | SO4 |
| 4 | 64 | 0.55 | 0.88 | 15 | SO4 |
| 5 | 302 | 0.54 | 0.75 | 39 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1786 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1771 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 855 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 842 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 798 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5ONA · Drosophila bag-of-marbles cbm peptide bound to human CAF40-CNOT1 · the same entry in another collection · chain F against F, 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
- Q92600 · AlphaFold monomer V2.0 prediction for CCR4-not transcription complex subunit 9 (Q92600) · a predicted model of the same protein · chain B against A, TM-score 0.96
- P22745 · AlphaFold monomer V2.0 prediction for protein bag-of-marbles (P22745) · a predicted model of the same protein · chain F against A, TM-score 0.76
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 Q92600
- Every structure of UniProt P22745
- Elsewhere: RCSB PDB 5ONA · PDBe 5ONA · UniProt A5YKK6 · UniProt Q92600 · UniProt P22745
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