Research workbench
Crystal structure apo CDK2/CYCLIN a
Analyse Crystal structure apo CDK2/CYCLIN a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IF1
- Type
- protein
- Length
- 1,108 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 2; Cyclin-A2
- EC
- 2.7.11.22
- UniProt
- P24941, P20248
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 298 | 34% helix, 17% strand | P24941 |
| B, D | Cyclin-A2 | protein | 257 | 62% helix, 0% strand | P20248 |
| C | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 296 | 32% helix, 17% strand | P24941 |
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.82 | 0.99 | 24 | empty |
| 2 | 125 | 0.79 | 0.97 | 24 | empty |
| 3 | 839 | 0.75 | 0.79 | 88 | empty |
| 4 | 273 | 0.69 | 0.84 | 27 | empty |
| 5 | 356 | 0.66 | 0.80 | 45 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1636 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1557 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 466 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 463 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 78 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5IF1 · Crystal structure apo CDK2/cyclin A · the same entry in another collection · chain D against D, TM-score 1.00
- P20248 · AlphaFold monomer V2.0 prediction for cyclin-A2 (P20248) · a predicted model of the same protein · chain D against A, TM-score 1.00
- 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 P20248
- Elsewhere: RCSB PDB 5IF1 · PDBe 5IF1 · UniProt P24941 · UniProt P20248
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