Research workbench
Yeast NOT1 CN9BD-CAF40 complex
Analyse Yeast NOT1 CN9BD-CAF40 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CV5
- Type
- protein
- Length
- 891 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- General negative regulator of transcription subunit 1; Protein CAF40
- UniProt
- P25655, P53829
- Ligands
- TBR
- Pockets
- 13 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | General negative regulator of transcription subunit 1 | protein | 185 | 73% helix, 0% strand | P25655 |
| B | Protein CAF40 | protein | 260 | 71% helix, 0% strand | P53829 |
| D | Protein CAF40 | protein | 261 | 72% helix, 0% strand | P53829 |
Ligands and binding sites
- TBR · Hexatantalum dodecabromide · ligand · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 487 | 0.65 | 0.77 | 47 | empty |
| 2 | 197 | 0.64 | 0.84 | 29 | empty |
| 3 | 307 | 0.59 | 0.78 | 37 | empty |
| 4 | 320 | 0.57 | 0.76 | 38 | empty |
| 5 | 188 | 0.57 | 0.80 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1139 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1091 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 435 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4CV5 · yeast NOT1 CN9BD-CAF40 complex · the same entry in another collection · chain A against A, TM-score 1.00
- P53829 · AlphaFold monomer V2.0 prediction for protein CAF40 (P53829) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P25655 · AlphaFold monomer V2.0 prediction for general negative regulator of transcription subunit… · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P25655
- Every structure of UniProt P53829
- Elsewhere: RCSB PDB 4CV5 · PDBe 4CV5 · UniProt P25655 · UniProt P53829
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