MolNFT v1 · #180274 · protein
Cryoem structure of yeast tfiik (KIN28/CCL1/TFB3) complex
7KUE · RNA polymerase II transcription factor B subunit 3: “Cryoem structure of yeast tfiik (KIN28/CCL1/TFB3) complex”. Electron microscopy, 2 ligands (ADP, AF3), 7 pockets (best druggability 0.82). MolNFT v1 #180274 on GenesisL1: 3D…
- PDB
- 7KUE
- Type
- protein
- Length
- 577 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA polymerase II transcription factor B subunit 3; SERINE/THREONINE-protein kinase…
- EC
- 2.7.11.23
- UniProt
- Q03290, P06242, P37366
- Ligands
- ADP, AF3
- Pockets
- 7 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 41% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | RNA polymerase II transcription factor B subunit 3 | protein | 62 | 29% helix, 0% strand | Q03290 |
| A | SERINE/THREONINE-protein kinase KIN28 (EC 2.7.11.23) | protein | 290 | 27% helix, 7% strand | P06242 |
| B | Cyclin CCL1 | protein | 225 | 62% helix, 0% strand | P37366 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.82 | 0.83 | 112 | empty |
| 2 | 67 | 0.61 | 0.91 | 16 | empty |
| 3 | 286 | 0.57 | 0.77 | 30 | ADP |
| 4 | 227 | 0.56 | 0.78 | 27 | empty |
| 5 | 54 | 0.35 | 0.78 | 11 | empty |
Interfaces
3 interfaces between chains.
- C–B · 1275 Ų buried · 9 hydrogen bonds · protein-protein
- C–A · 1136 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1042 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 7KUE · CryoEM structure of Yeast TFIIK (Kin28/Ccl1/Tfb3) Complex · the same entry in another collection · chain C against C, TM-score 1.00
- P37366 · AlphaFold monomer V2.0 prediction for cyclin CCL1 (P37366) · a predicted model of the same protein · chain B against A, TM-score 0.96
- P06242 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase KIN28 (P06242) · a predicted model of the same protein · chain A against A, TM-score 0.96
- Q03290 · AlphaFold monomer V2.0 prediction for RNA polymerase II transcription factor B subunit 3… · a predicted model of the same protein · chain C against A, TM-score 0.69
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 Q03290
- Every structure of UniProt P06242
- Every structure of UniProt P37366
- Elsewhere: RCSB PDB 7KUE · PDBe 7KUE · UniProt Q03290 · UniProt P06242 · UniProt P37366
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