Research workbench
Crystal structure of human CDK12/CYCLIN K in complex with ADP-aluminum fluoride
Analyse Crystal structure of human CDK12/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
- 4NST
- Type
- protein
- Length
- 1,128 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 12; Cyclin-K
- EC
- 2.7.11.22, 2.7.11.23
- UniProt
- Q9NYV4, O75909
- Ligands
- ADP, AF3, MG
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 12 (EC 2.7.11.22, 2.7.11.23) | protein | 323 | 35% helix, 15% strand | Q9NYV4 |
| B | Cyclin-K | protein | 246 | 66% helix, 0% strand | O75909 |
| C | Cyclin-dependent kinase 12 (EC 2.7.11.22, 2.7.11.23) | protein | 318 | 36% helix, 15% strand | Q9NYV4 |
| D | Cyclin-K | protein | 241 | 66% 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 · 7 copies · chains A, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.75 | 0.88 | 34 | ADP, AF3, MG |
| 2 | 262 | 0.71 | 0.86 | 32 | ADP, AF3, MG |
| 3 | 662 | 0.70 | 0.77 | 75 | empty |
| 4 | 444 | 0.64 | 0.78 | 48 | MG |
| 5 | 228 | 0.55 | 0.77 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1131 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1070 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 501 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 451 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 89 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 4NST · Crystal structure of human Cdk12/Cyclin K in complex with ADP-aluminum fluoride · the same entry in another collection · chain D against D, TM-score 1.00
- Q9NYV4 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 12 (Q9NYV4) · 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 Q9NYV4
- Every structure of UniProt O75909
- Elsewhere: RCSB PDB 4NST · PDBe 4NST · UniProt Q9NYV4 · UniProt O75909
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