Research workbench
Crystal structure of human CDK8/CYCC
Analyse Crystal structure of human CDK8/CYCC in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RGF
- Type
- protein
- Length
- 587 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 8; Cyclin-C
- EC
- 2.7.11.22, 2.7.11.23
- UniProt
- P49336, P24863
- Ligands
- BAX
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 8 (EC 2.7.11.22, 2.7.11.23) | protein | 321 | 42% helix, 11% strand | P49336 |
| B | Cyclin-C | protein | 266 | 69% helix, 0% strand | P24863 |
Ligands and binding sites
- BAX · 4-{4-[({[4-chloro-3-(trifluoromethyl)phenyl]amino}carbonyl)amino]phenoxy}-N-methylpyridine-2-carboxamide · ligand · chains A
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.70 | 0.85 | 37 | BAX |
| 2 | 174 | 0.58 | 0.81 | 30 | EDO |
| 3 | 221 | 0.55 | 0.78 | 23 | EDO |
| 4 | 148 | 0.50 | 0.79 | 24 | empty |
| 5 | 170 | 0.45 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1778 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3RGF · Crystal Structure of human CDK8/CycC · the same entry in another collection · chain A against A, TM-score 1.00
- P24863 · AlphaFold monomer V2.0 prediction for cyclin-C (P24863) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P49336 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 8 (P49336) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P49336
- Every structure of UniProt P24863
- Elsewhere: RCSB PDB 3RGF · PDBe 3RGF · UniProt P49336 · UniProt P24863
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