Research workbench
Crystal structure of human CDK13/CYCLIN K in complex with ADP-aluminum fluoride
Analyse Crystal structure of human CDK13/CYCLIN K in complex with ADP-aluminum fluoride in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EFQ
- Type
- protein
- Length
- 1,129 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 13; Cyclin-K
- EC
- 2.7.11.22, 2.7.11.23
- UniProt
- Q14004, O75909
- Ligands
- ADP, AF3, MG
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 13 (EC 2.7.11.22, 2.7.11.23) | protein | 322 | 36% helix, 15% strand | Q14004 |
| B | Cyclin-K | protein | 242 | 66% helix, 0% strand | O75909 |
| C | Cyclin-dependent kinase 13 (EC 2.7.11.22, 2.7.11.23) | protein | 326 | 37% helix, 14% strand | Q14004 |
| D | Cyclin-K | protein | 239 | 67% helix, 0% strand | O75909 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, C
- AF3 · Aluminum fluoride · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.74 | 0.87 | 30 | ADP |
| 2 | 938 | 0.73 | 0.77 | 81 | empty |
| 3 | 1180 | 0.73 | 0.76 | 123 | empty |
| 4 | 263 | 0.73 | 0.87 | 34 | ADP, AF3, MG |
| 5 | 164 | 0.55 | 0.80 | 30 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1058 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 913 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 452 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 386 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 107 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 5EFQ · Crystal structure of human Cdk13/Cyclin K in complex with ADP-aluminum fluoride · the same entry in another collection · chain D against D, TM-score 1.00
- Q14004 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 13 (Q14004) · a predicted model of the same protein · chain C against A, TM-score 0.99
- O75909 · AlphaFold monomer V2.0 prediction for cyclin-K (O75909) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q14004
- Every structure of UniProt O75909
- Elsewhere: RCSB PDB 5EFQ · PDBe 5EFQ · UniProt Q14004 · UniProt O75909
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