MolNFT v1 · #170214 · protein
Crystal structure of CDK8-cycc in complex with BI00690300
6Y0A · Cyclin-dependent kinase 8: “Crystal structure of CDK8-cycc in complex with BI00690300”. X-ray diffraction, 1 ligand (JRE), 13 pockets (best druggability 0.71). MolNFT v1 #170214 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6Y0A
- Type
- protein
- Length
- 613 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
- JRE
- Pockets
- 13 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 8 (EC 2.7.11.22, 2.7.11.23) | protein | 346 | 41% helix, 12% strand | P49336 |
| B | Cyclin-C | protein | 267 | 68% helix, 0% strand | P24863 |
Ligands and binding sites
- JRE · 6-[5-chloranyl-4-[(1~{S})-1-oxidanylethyl]pyridin-3-yl]-3,4-dihydro-2~{H}-1,8-naphthyridine-1-carboxamide · ligand · chains A
- FMT · Formic acid · additive · 3 copies · chains B, A
- EDO · 1,2-ethanediol · additive · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.71 | 0.97 | 22 | FMT |
| 2 | 466 | 0.67 | 0.79 | 38 | JRE |
| 3 | 202 | 0.66 | 0.85 | 31 | FMT |
| 4 | 193 | 0.57 | 0.80 | 23 | empty |
| 5 | 122 | 0.53 | 0.82 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2002 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6Y0A · CRYSTAL STRUCTURE OF CDK8-CycC IN COMPLEX WITH BI00690300 · 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 0.98
- 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 0.97
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 6Y0A · PDBe 6Y0A · UniProt P49336 · UniProt P24863
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