Research workbench
Yeast tfiik (KIN28/CCL1/TFB3) complex
Analyse Yeast tfiik (KIN28/CCL1/TFB3) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XI8
- Type
- protein
- Length
- 636 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
- 8 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 42% 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 | 284 | 61% helix, 0% strand | P37366 |
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 | 1099 | 0.82 | 0.83 | 116 | empty |
| 2 | 63 | 0.59 | 0.91 | 17 | empty |
| 3 | 275 | 0.55 | 0.76 | 31 | ADP |
| 4 | 217 | 0.55 | 0.78 | 25 | empty |
| 5 | 198 | 0.50 | 0.76 | 34 | empty |
Interfaces
3 interfaces between chains.
- C–B · 1280 Ų buried · 9 hydrogen bonds · protein-protein
- C–A · 1141 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1035 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6XI8 · Yeast TFIIK (Kin28/Ccl1/Tfb3) Complex · the same entry in another collection · chain C against C, TM-score 1.00
- 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
- P37366 · AlphaFold monomer V2.0 prediction for cyclin CCL1 (P37366) · a predicted model of the same protein · chain B against A, TM-score 0.93
- 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 6XI8 · PDBe 6XI8 · UniProt Q03290 · UniProt P06242 · UniProt P37366
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