MolNFT v1 · #179097 · protein
Crystal structure of the yeast RNA pol II ctd kinase ctdk-1 complex
7JV7 · Ctd kinase subunit alpha: “Crystal structure of the yeast RNA pol II ctd kinase ctdk-1 complex”. X-ray diffraction, 9 pockets (best druggability 0.75). MolNFT v1 #179097 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7JV7
- Type
- protein
- Length
- 864 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ctd kinase subunit alpha; Ctd kinase subunit beta; Ctd kinase subunit gamma
- EC
- 2.7.11.23
- UniProt
- Q03957, P46962, P46963
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ctd kinase subunit alpha (EC 2.7.11.23) | protein | 304 | 34% helix, 17% strand | Q03957 |
| B | Ctd kinase subunit beta | protein | 310 | 63% helix, 4% strand | P46962 |
| C | Ctd kinase subunit gamma | protein | 250 | 69% helix, 0% strand | P46963 |
Ligands and binding sites
- FLC · Citrate anion · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1121 | 0.75 | 0.78 | 72 | FLC |
| 2 | 324 | 0.62 | 0.79 | 44 | empty |
| 3 | 255 | 0.61 | 0.80 | 32 | empty |
| 4 | 371 | 0.57 | 0.75 | 42 | empty |
| 5 | 64 | 0.54 | 0.88 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2119 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1983 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 1407 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7JV7 · Crystal Structure of the yeast RNA Pol II CTD kinase CTDK-1 complex · the same entry in another collection · chain C against C, TM-score 1.00
- Q03957 · AlphaFold monomer V2.0 prediction for ctd kinase subunit alpha (Q03957) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P46962 · AlphaFold monomer V2.0 prediction for ctd kinase subunit beta (P46962) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P46963 · AlphaFold monomer V2.0 prediction for ctd kinase subunit gamma (P46963) · a predicted model of the same protein · chain C against A, TM-score 0.80
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 Q03957
- Every structure of UniProt P46962
- Every structure of UniProt P46963
- Elsewhere: RCSB PDB 7JV7 · PDBe 7JV7 · UniProt Q03957 · UniProt P46962 · UniProt P46963
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