MolNFT v1 · #59034 · protein
Crystal structure of human CDK9/CYCLINT1
3BLH · Cell division protein kinase 9: “Crystal structure of human CDK9/CYCLINT1”. X-ray diffraction, 9 pockets (best druggability 0.61). MolNFT v1 #59034 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3BLH
- Type
- protein
- Length
- 547 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 9; Cyclin-T1
- EC
- 2.7.11.22, 2.7.11.23
- UniProt
- P50750, O60563
- Pockets
- 9 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division protein kinase 9 (EC 2.7.11.22, 2.7.11.23) | protein | 292 | 36% helix, 17% strand | P50750 |
| B | Cyclin-T1 | protein | 255 | 65% helix, 0% strand | O60563 |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 239 | 0.61 | 0.80 | 36 | empty |
| 2 | 86 | 0.54 | 0.85 | 27 | empty |
| 3 | 182 | 0.51 | 0.77 | 27 | empty |
| 4 | 151 | 0.49 | 0.78 | 25 | empty |
| 5 | 98 | 0.44 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1002 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 3BLH · Crystal Structure of Human CDK9/cyclinT1 · the same entry in another collection · chain A against A, TM-score 1.00
- P50750 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 9 (P50750) · a predicted model of the same protein · chain A against A, TM-score 0.98
- O60563 · AlphaFold monomer V2.0 prediction for cyclin-T1 (O60563) · a predicted model of the same protein · chain B 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 P50750
- Every structure of UniProt O60563
- Elsewhere: RCSB PDB 3BLH · PDBe 3BLH · UniProt P50750 · UniProt O60563
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