Research workbench
Crystal structure of human CDK2-SPY1-P27 ternary complex
Analyse Crystal structure of human CDK2-SPY1-P27 ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UQ3
- Type
- protein
- Length
- 451 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 2; Speedy protein a; Cyclin-dependent kinase inhibitor 1B
- EC
- 2.7.11.22
- UniProt
- P24941, Q5MJ70, P46527
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 270 | 35% helix, 7% strand | P24941 |
| B | Speedy protein a | protein | 135 | 57% helix, 0% strand | Q5MJ70 |
| C | Cyclin-dependent kinase inhibitor 1B | protein | 46 | 24% helix, 0% strand | P46527 |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.64 | 0.80 | 46 | empty |
| 2 | 129 | 0.53 | 0.81 | 20 | empty |
| 3 | 69 | 0.47 | 0.83 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1446 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1335 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 104 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5UQ3 · Crystal structure of human Cdk2-Spy1-P27 ternary complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q5MJ70 · AlphaFold monomer V2.0 prediction for speedy protein a (Q5MJ70) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P24941 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 2 (P24941) · a predicted model of the same protein · chain A against A, TM-score 0.89
- P46527 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase inhibitor 1B (P46527) · a predicted model of the same protein · chain C against A, TM-score 0.83
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 P24941
- Every structure of UniProt Q5MJ70
- Every structure of UniProt P46527
- Elsewhere: RCSB PDB 5UQ3 · PDBe 5UQ3 · UniProt P24941 · UniProt Q5MJ70 · UniProt P46527
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.