Research workbench
Crystal structure of human CDK2-SPY1 complex
Analyse Crystal structure of human CDK2-SPY1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UQ1
- Type
- protein
- Length
- 850 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 2; Speedy protein a
- EC
- 2.7.11.22
- UniProt
- P24941, Q5MJ70
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 288 | 32% helix, 14% strand | P24941 |
| B | Speedy protein a | protein | 134 | 64% helix, 0% strand | Q5MJ70 |
| C | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 289 | 31% helix, 17% strand | P24941 |
| D | Speedy protein a | protein | 139 | 62% helix, 0% strand | Q5MJ70 |
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 695 | 0.77 | 0.82 | 68 | empty |
| 2 | 446 | 0.69 | 0.80 | 48 | empty |
| 3 | 440 | 0.67 | 0.79 | 52 | empty |
| 4 | 400 | 0.62 | 0.77 | 25 | empty |
| 5 | 257 | 0.54 | 0.76 | 28 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1414 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1399 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1342 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 51 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5UQ1 · Crystal structure of human Cdk2-Spy1 complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q5MJ70 · AlphaFold monomer V2.0 prediction for speedy protein a (Q5MJ70) · a predicted model of the same protein · chain D against A, TM-score 0.99
- 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 0.92
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
- Elsewhere: RCSB PDB 5UQ1 · PDBe 5UQ1 · UniProt P24941 · UniProt Q5MJ70
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